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539 lines
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<title>cristallina package — cristallina 0.0.post1.dev53+g9be81e9.d20230129 documentation</title>
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<section id="cristallina-package">
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<h1>cristallina package<a class="headerlink" href="#cristallina-package" title="Permalink to this heading">¶</a></h1>
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<section id="submodules">
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<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this heading">¶</a></h2>
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</section>
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<section id="module-cristallina.SEA_GraphClient">
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<span id="cristallina-sea-graphclient-module"></span><h2>cristallina.SEA_GraphClient module<a class="headerlink" href="#module-cristallina.SEA_GraphClient" title="Permalink to this heading">¶</a></h2>
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<p>client for SEA GraphServer</p>
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<p>Usage:</p>
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<p># open a client to host ‘samenv’, port 8764
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# the port number for the graph server may be retrived by
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# the command ‘sea list’ on the samenv machine</p>
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<p>client = GraphClient(‘samenv:8764’)</p>
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<p># get one curve</p>
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<p>tlist, vlist, period = client.get_curves(start, end, name)</p>
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<p>or</p>
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<p># get all important curves
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curves = client.get_curves(start, end)</p>
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<p># where:</p>
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<blockquote>
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<div><p>start, end: interval (unix time, as retrieved from time.time())
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name: the name of a curve (if no name or a list of names</p>
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<blockquote>
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<div><p>is given, the result is a curves dict)</p>
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</div></blockquote>
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<p>curves: dict <name> of [tlist, vlist, period]
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tlist: time axis (unix time)
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vlist: values (y-axis)
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period: the expected resolution (a hint for graphic clients,</p>
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<blockquote>
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<div><p>saying that for a time step t(n) - t(n-1) significantly
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bigger than period, an additional point should be added
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at t(n) - period)</p>
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</div></blockquote>
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</div></blockquote>
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<dl class="py class">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.GraphClient">
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<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cristallina.SEA_GraphClient.</span></span><span class="sig-name descname"><span class="pre">GraphClient</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hostport</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#GraphClient"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.GraphClient" title="Permalink to this definition">¶</a></dt>
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<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3.10/library/functions.html#object" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
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<dl class="py method">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.GraphClient.close">
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<span class="sig-name descname"><span class="pre">close</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#GraphClient.close"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.GraphClient.close" title="Permalink to this definition">¶</a></dt>
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<dd></dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.GraphClient.get_curves">
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<span class="sig-name descname"><span class="pre">get_curves</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">none_value</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nmax</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/cristallina/SEA_GraphClient.html#GraphClient.get_curves"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.GraphClient.get_curves" title="Permalink to this definition">¶</a></dt>
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<dd><p>get curves</p>
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<dl class="simple">
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<dt>start, end: interval (unix time, as retrieved from time.time())</dt><dd><p>non positive values are taken relative to the current time</p>
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</dd>
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</dl>
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<p>name: a single name or a list of names or None to get all curves (as shown in the SEA GUI)
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none_value: replacement when no value is defined
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nmax: max. number of points per curve</p>
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<p>when name is a string, returns [tlist, vlist, period]
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when name is None or a list of strings (names) returns a dict <name> of [tlist, vlist, period]</p>
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<p>tlist: time axis (unix time)
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vlist: values (y-axis)
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period: the expected resolution (a hint for graphic clients)</p>
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</dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.GraphClient.get_names">
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<span class="sig-name descname"><span class="pre">get_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</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/cristallina/SEA_GraphClient.html#GraphClient.get_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.GraphClient.get_names" title="Permalink to this definition">¶</a></dt>
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<dd><p>get names and properties of curves configured to be display on SEA GUI graphics</p>
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</dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.GraphClient.get_raw">
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<span class="sig-name descname"><span class="pre">get_raw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">end</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#GraphClient.get_raw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.GraphClient.get_raw" title="Permalink to this definition">¶</a></dt>
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<dd><p>get raw curves (values as text)</p>
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</dd></dl>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.expect_reply">
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<span class="sig-prename descclassname"><span class="pre">cristallina.SEA_GraphClient.</span></span><span class="sig-name descname"><span class="pre">expect_reply</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sock</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">expected</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#expect_reply"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.expect_reply" title="Permalink to this definition">¶</a></dt>
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<dd></dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.raw_sics_client">
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<span class="sig-prename descclassname"><span class="pre">cristallina.SEA_GraphClient.</span></span><span class="sig-name descname"><span class="pre">raw_sics_client</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hostport</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">login</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#raw_sics_client"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.raw_sics_client" title="Permalink to this definition">¶</a></dt>
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<dd></dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.SEA_GraphClient.sics_client">
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<span class="sig-prename descclassname"><span class="pre">cristallina.SEA_GraphClient.</span></span><span class="sig-name descname"><span class="pre">sics_client</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">hostport</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">command</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">login</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Spy</span> <span class="pre">007'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/SEA_GraphClient.html#sics_client"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.SEA_GraphClient.sics_client" title="Permalink to this definition">¶</a></dt>
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<dd></dd></dl>
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</section>
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<section id="module-cristallina.analysis">
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<span id="cristallina-analysis-module"></span><h2>cristallina.analysis module<a class="headerlink" href="#module-cristallina.analysis" title="Permalink to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.analysis.fit_2d_gaussian">
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<span class="sig-prename descclassname"><span class="pre">cristallina.analysis.</span></span><span class="sig-name descname"><span class="pre">fit_2d_gaussian</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">image</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cristallina.utils.ROI" title="cristallina.utils.ROI"><span class="pre">ROI</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/analysis.html#fit_2d_gaussian"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.analysis.fit_2d_gaussian" title="Permalink to this definition">¶</a></dt>
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<dd><p>2D Gaussian fit using LMFit for a given image and an optional region of interest.</p>
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<p>Returns the x, y coordinates of the center and the results object which contains
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further fit statistics.</p>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.analysis.get_contrast_images">
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<span class="sig-prename descclassname"><span class="pre">cristallina.analysis.</span></span><span class="sig-name descname"><span class="pre">get_contrast_images</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">fileset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'JF16T03V01'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">alignment_channels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">roi</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#cristallina.utils.ROI" title="cristallina.utils.ROI"><span class="pre">ROI</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">preview</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/analysis.html#get_contrast_images"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.analysis.get_contrast_images" title="Permalink to this definition">¶</a></dt>
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<dd><p>See perform_image_calculations. Here calculates mean and standard deviation for a given set of images.</p>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.analysis.setup_cachedirs">
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<span class="sig-prename descclassname"><span class="pre">cristallina.analysis.</span></span><span class="sig-name descname"><span class="pre">setup_cachedirs</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pgroup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cachedir</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/cristallina/analysis.html#setup_cachedirs"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.analysis.setup_cachedirs" title="Permalink to this definition">¶</a></dt>
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<dd><p>Sets the path to a persistent cache directory either from the given p-group (e.g. “p20841”)
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or an explicitly given directory.</p>
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<p>If heuristics fail we use “/tmp” as a non-persistent alternative.</p>
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</dd></dl>
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</section>
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<section id="module-cristallina.config">
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<span id="cristallina-config-module"></span><h2>cristallina.config module<a class="headerlink" href="#module-cristallina.config" title="Permalink to this heading">¶</a></h2>
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</section>
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<section id="module-cristallina.plot">
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<span id="cristallina-plot-module"></span><h2>cristallina.plot module<a class="headerlink" href="#module-cristallina.plot" title="Permalink to this heading">¶</a></h2>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.plot.axis_styling">
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<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">axis_styling</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/plot.html#axis_styling"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.axis_styling" title="Permalink to this definition">¶</a></dt>
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<dd></dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.plot.ju_patch_less_verbose">
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<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">ju_patch_less_verbose</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ju_module</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/plot.html#ju_patch_less_verbose"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.ju_patch_less_verbose" title="Permalink to this definition">¶</a></dt>
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<dd><p>Quick monkey patch to suppress verbose messages from gain & pedestal file searcher.</p>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.plot.plot_1d_channel">
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<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_1d_channel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SFDataFiles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</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/cristallina/plot.html#plot_1d_channel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_1d_channel" title="Permalink to this definition">¶</a></dt>
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<dd><p>Plots channel data for a channel that contains a single numeric value per pulse.</p>
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</dd></dl>
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<dl class="py function">
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<dt class="sig sig-object py" id="cristallina.plot.plot_2d_channel">
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<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_2d_channel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SFDataFiles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</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/cristallina/plot.html#plot_2d_channel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_2d_channel" title="Permalink to this definition">¶</a></dt>
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<dd><p>Plots channel data for a channel that contains a 1d array of numeric values per pulse.</p>
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</dd></dl>
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<dl class="py function">
|
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<dt class="sig sig-object py" id="cristallina.plot.plot_channel">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_channel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SFDataFiles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</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/cristallina/plot.html#plot_channel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_channel" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Plots a given channel from an SFDataFiles object.</p>
|
||
<p>Optionally: a matplotlib axis to plot into</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.plot.plot_correlation">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_correlation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">ax_kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/plot.html#plot_correlation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_correlation" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Plots the correlation of x and y in a normalized scatterplot.
|
||
If no axis is given a figure and axis are created.</p>
|
||
<dl class="simple">
|
||
<dt>Returns: The axis object and the correlation coefficient between</dt><dd><p>x and y.</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.plot.plot_image_channel">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_image_channel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SFDataFiles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pulse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rois</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">norms</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/cristallina/plot.html#plot_image_channel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_image_channel" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Plots channel data for a channel that contains an image (2d array) of numeric values per pulse.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.plot.plot_spectrum_channel">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.plot.</span></span><span class="sig-name descname"><span class="pre">plot_spectrum_channel</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">SFDataFiles</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name_x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">channel_name_y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">average</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pulse</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</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/cristallina/plot.html#plot_spectrum_channel"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.plot.plot_spectrum_channel" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Plots channel data for two channels where the first is taken as the (constant) x-axis
|
||
and the second as the y-axis (here we take by default the mean over the individual pulses).</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="module-cristallina.skeleton">
|
||
<span id="cristallina-skeleton-module"></span><h2>cristallina.skeleton module<a class="headerlink" href="#module-cristallina.skeleton" title="Permalink to this heading">¶</a></h2>
|
||
<p>This is a skeleton file that can serve as a starting point for a Python
|
||
console script. To run this script uncomment the following lines in the
|
||
<code class="docutils literal notranslate"><span class="pre">[options.entry_points]</span></code> section in <code class="docutils literal notranslate"><span class="pre">setup.cfg</span></code>:</p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">console_scripts</span> <span class="o">=</span>
|
||
<span class="n">fibonacci</span> <span class="o">=</span> <span class="n">cristallina</span><span class="o">.</span><span class="n">skeleton</span><span class="p">:</span><span class="n">run</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Then run <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">.</span></code> (or <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">-e</span> <span class="pre">.</span></code> for editable mode)
|
||
which will install the command <code class="docutils literal notranslate"><span class="pre">fibonacci</span></code> inside your current environment.</p>
|
||
<p>Besides console scripts, the header (i.e. until <code class="docutils literal notranslate"><span class="pre">_logger</span></code>…) of this file can
|
||
also be used as template for Python modules.</p>
|
||
<div class="admonition note">
|
||
<p class="admonition-title">Note</p>
|
||
<p>This file can be renamed depending on your needs or safely removed if not needed.</p>
|
||
</div>
|
||
<p class="rubric">References</p>
|
||
<ul class="simple">
|
||
<li><p><a class="reference external" href="https://setuptools.pypa.io/en/latest/userguide/entry_point.html">https://setuptools.pypa.io/en/latest/userguide/entry_point.html</a></p></li>
|
||
<li><p><a class="reference external" href="https://pip.pypa.io/en/stable/reference/pip_install">https://pip.pypa.io/en/stable/reference/pip_install</a></p></li>
|
||
</ul>
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.skeleton.fib">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.skeleton.</span></span><span class="sig-name descname"><span class="pre">fib</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">n</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/skeleton.html#fib"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.skeleton.fib" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Fibonacci example function</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>n</strong> (<a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a>) – integer</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>n-th Fibonacci number</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)">int</a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.skeleton.main">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.skeleton.</span></span><span class="sig-name descname"><span class="pre">main</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/skeleton.html#main"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.skeleton.main" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Wrapper allowing <a class="reference internal" href="#cristallina.skeleton.fib" title="cristallina.skeleton.fib"><code class="xref py py-func docutils literal notranslate"><span class="pre">fib()</span></code></a> to be called with string arguments in a CLI fashion</p>
|
||
<p>Instead of returning the value from <a class="reference internal" href="#cristallina.skeleton.fib" title="cristallina.skeleton.fib"><code class="xref py py-func docutils literal notranslate"><span class="pre">fib()</span></code></a>, it prints the result to the
|
||
<code class="docutils literal notranslate"><span class="pre">stdout</span></code> in a nicely formatted message.</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>args</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3.10/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>]</em>) – command line parameters as list of strings
|
||
(for example <code class="docutils literal notranslate"><span class="pre">["--verbose",</span> <span class="pre">"42"]</span></code>).</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.skeleton.parse_args">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.skeleton.</span></span><span class="sig-name descname"><span class="pre">parse_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">args</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/skeleton.html#parse_args"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.skeleton.parse_args" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Parse command line parameters</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>args</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/3.10/library/stdtypes.html#str" title="(in Python v3.10)"><em>str</em></a><em>]</em>) – command line parameters as list of strings
|
||
(for example <code class="docutils literal notranslate"><span class="pre">["--help"]</span></code>).</p>
|
||
</dd>
|
||
<dt class="field-even">Returns<span class="colon">:</span></dt>
|
||
<dd class="field-even"><p>command line parameters namespace</p>
|
||
</dd>
|
||
<dt class="field-odd">Return type<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.10/library/argparse.html#argparse.Namespace" title="(in Python v3.10)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a></p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.skeleton.run">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.skeleton.</span></span><span class="sig-name descname"><span class="pre">run</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/skeleton.html#run"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.skeleton.run" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Calls <a class="reference internal" href="#cristallina.skeleton.main" title="cristallina.skeleton.main"><code class="xref py py-func docutils literal notranslate"><span class="pre">main()</span></code></a> passing the CLI arguments extracted from <a class="reference external" href="https://docs.python.org/3.10/library/sys.html#sys.argv" title="(in Python v3.10)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sys.argv</span></code></a></p>
|
||
<p>This function can be used as entry point to create console scripts with setuptools.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.skeleton.setup_logging">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.skeleton.</span></span><span class="sig-name descname"><span class="pre">setup_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">loglevel</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/skeleton.html#setup_logging"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.skeleton.setup_logging" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Setup basic logging</p>
|
||
<dl class="field-list simple">
|
||
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
|
||
<dd class="field-odd"><p><strong>loglevel</strong> (<a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><em>int</em></a>) – minimum loglevel for emitting messages</p>
|
||
</dd>
|
||
</dl>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="module-cristallina.utils">
|
||
<span id="cristallina-utils-module"></span><h2>cristallina.utils module<a class="headerlink" href="#module-cristallina.utils" title="Permalink to this heading">¶</a></h2>
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.FWHM_to_sigma">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">FWHM_to_sigma</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">FWHM</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#FWHM_to_sigma"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.FWHM_to_sigma" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>FWHM to gaussian sigma</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py class">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI">
|
||
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">ROI</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">left</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">right</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">top</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bottom</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center_x</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center_y</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/functions.html#int" title="(in Python v3.10)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">name</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3.10/library/stdtypes.html#str" title="(in Python v3.10)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3.10/library/constants.html#None" title="(in Python v3.10)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#ROI"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.ROI" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3.10/library/functions.html#object" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
|
||
<p>Definition of region of interest (ROI) in image coordinates.</p>
|
||
<p>Example: ROI(left=10, right=20, bottom=100, top=200).</p>
|
||
<p>Directions assume that lower left corner of image is at (x=0, y=0).</p>
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.LeftRightBottomTop">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">LeftRightBottomTop</span></span><a class="headerlink" href="#cristallina.utils.ROI.LeftRightBottomTop" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.cols">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">cols</span></span><a class="headerlink" href="#cristallina.utils.ROI.cols" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py method">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.from_centers_widths">
|
||
<span class="sig-name descname"><span class="pre">from_centers_widths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">center_x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">center_y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">width</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">height</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#ROI.from_centers_widths"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.ROI.from_centers_widths" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.height">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">height</span></span><a class="headerlink" href="#cristallina.utils.ROI.height" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.rows">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">rows</span></span><a class="headerlink" href="#cristallina.utils.ROI.rows" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
<dl class="py property">
|
||
<dt class="sig sig-object py" id="cristallina.utils.ROI.width">
|
||
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">width</span></span><a class="headerlink" href="#cristallina.utils.ROI.width" title="Permalink to this definition">¶</a></dt>
|
||
<dd></dd></dl>
|
||
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.channel_names">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">channel_names</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">run_number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#channel_names"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.channel_names" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Prints channel names for a given run_number or scan object</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.eV_to_joules">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">eV_to_joules</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">eV</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#eV_to_joules"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.eV_to_joules" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Just a unit conversion</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.find_nearest">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">find_nearest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#find_nearest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.find_nearest" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Finds an index in an array with a value that is nearest to given number</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.find_two_nearest">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">find_two_nearest</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">time_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">percentage</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#find_two_nearest"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.find_two_nearest" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Finds indeces of the two values that are the nearest to the given value in an array</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.gauss">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">gauss</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">H</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">A</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">x0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#gauss"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.gauss" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Returns gauss function value</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.gauss_fit">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">gauss_fit</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">x</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">y</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fit_details</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</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/cristallina/utils.html#gauss_fit"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.gauss_fit" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Returns [baseline_offset, Amplitude, center, sigma, FWHM]</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.heuristic_extract_base_path">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">heuristic_extract_base_path</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#heuristic_extract_base_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.heuristic_extract_base_path" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>The function tries to guess the full path where the raw data is saved.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.heuristic_extract_pgroup">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">heuristic_extract_pgroup</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</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/cristallina/utils.html#heuristic_extract_pgroup"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.heuristic_extract_pgroup" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>The function tries to guess the current p-group from the
|
||
current working directory (default) or the contents of
|
||
the given path.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.heuristic_extract_smalldata_path">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">heuristic_extract_smalldata_path</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#heuristic_extract_smalldata_path"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.heuristic_extract_smalldata_path" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>The function tries to guess the full path where the small data is saved.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.joules_to_eV">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">joules_to_eV</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">joules</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#joules_to_eV"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.joules_to_eV" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Just a unit conversion</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.photon_energy_from_wavelength">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">photon_energy_from_wavelength</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">wavelength</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#photon_energy_from_wavelength"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.photon_energy_from_wavelength" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Returns photon energy in eV from wavelength in meters. Source <a class="reference external" href="https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator">https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator</a></p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.print_run_info">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">print_run_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">run_number</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">print_channels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extra_verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_path</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/cristallina/utils.html#print_run_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.print_run_info" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Prints overview of run information.</p>
|
||
<p>Extra verbose output contains all files and pids.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.process_run">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">process_run</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">run_number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rois</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">detector</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'JF16T03V01'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">calculate</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_shots</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">slice(None,</span> <span class="pre">None,</span> <span class="pre">None)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_jobs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">16</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#process_run"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.process_run" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Process rois for a given detector. Save the results small data in the res/small_data/run…
|
||
By default only sum of rois is calculated, [mean,std,img] can be added to the “calculate” optional parameter.</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.scan_info">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">scan_info</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">run_number</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">small_data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#scan_info"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.scan_info" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Returns SFScanInfo object for a given run number.
|
||
If there is are small data channels, they will be added (small_data=False to suppress their loading).</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.sigma_to_FWHM">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">sigma_to_FWHM</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">sigma</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#sigma_to_FWHM"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.sigma_to_FWHM" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Gaussian sigma to FWHM</p>
|
||
</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.wavelength_from_photon_energy">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">wavelength_from_photon_energy</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">Eph</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#wavelength_from_photon_energy"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.wavelength_from_photon_energy" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Returns wavelength in meters from photon energy in eV. Source <a class="reference external" href="https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator">https://www.kmlabs.com/en/wavelength-to-photon-energy-calculator</a></p>
|
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</dd></dl>
|
||
|
||
<dl class="py function">
|
||
<dt class="sig sig-object py" id="cristallina.utils.xray_transmission">
|
||
<span class="sig-prename descclassname"><span class="pre">cristallina.utils.</span></span><span class="sig-name descname"><span class="pre">xray_transmission</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">energy</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">thickness</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">material</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'Si'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">density</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/cristallina/utils.html#xray_transmission"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cristallina.utils.xray_transmission" title="Permalink to this definition">¶</a></dt>
|
||
<dd><p>Calculate x-ray tranmission for given energy, thickness and material. Default material is Si. Add material=element as a string for another material. Density as optional parameter</p>
|
||
</dd></dl>
|
||
|
||
</section>
|
||
<section id="module-cristallina">
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<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-cristallina" title="Permalink to this heading">¶</a></h2>
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