deploy: 27b03c8

Ameyanagi · Dec 19, 2023 · 1293775 · 1293775
commit 1293775
Show file tree

Hide file tree

Showing 72 changed files with 7,922 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +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: 877e0241dabf7061ccdcd6f5a54067c3
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/authors.doctree b/.doctrees/authors.doctree
diff --git a/.doctrees/contributing.doctree b/.doctrees/contributing.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/history.doctree b/.doctrees/history.doctree
diff --git a/.doctrees/ibr_xas.doctree b/.doctrees/ibr_xas.doctree
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.doctrees/installation.doctree b/.doctrees/installation.doctree
diff --git a/.doctrees/modules.doctree b/.doctrees/modules.doctree
diff --git a/.doctrees/readme.doctree b/.doctrees/readme.doctree
diff --git a/.doctrees/usage.doctree b/.doctrees/usage.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_modules/ibr_xas/ibr_xas.html b/_modules/ibr_xas/ibr_xas.html
diff --git a/_modules/index.html b/_modules/index.html
@@ -0,0 +1,112 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Overview: module code &mdash; IBR-XAS 0.1.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+
+
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
+        <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=01f34227"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            IBR-XAS
+          </a>
+              <div class="version">
+                0.1.0
+              </div>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../readme.html">Iterative Bragg peak Removal of X-ray Absorption Spectrum (IBR-XAS)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">ibr_xas</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../contributing.html">Contributing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../authors.html">Credits</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../history.html">History</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">IBR-XAS</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="ibr_xas/ibr_xas.html">ibr_xas.ibr_xas</a></li>
+</ul>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Ryuichi Shimogawa.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+
+</footer>
+        </div>
+      </div>
+    </section>
+  </div>
+  <script>
+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>
diff --git a/_sources/authors.rst.txt b/_sources/authors.rst.txt
@@ -0,0 +1 @@
+.. include:: ../AUTHORS.rst
diff --git a/_sources/contributing.rst.txt b/_sources/contributing.rst.txt
@@ -0,0 +1 @@
+.. include:: ../CONTRIBUTING.rst
diff --git a/_sources/history.rst.txt b/_sources/history.rst.txt
@@ -0,0 +1 @@
+.. include:: ../HISTORY.rst
diff --git a/_sources/ibr_xas.rst.txt b/_sources/ibr_xas.rst.txt
@@ -0,0 +1,29 @@
+ibr\_xas package
+================
+
+Submodules
+----------
+
+ibr\_xas.cli module
+-------------------
+
+.. automodule:: ibr_xas.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ibr\_xas.ibr\_xas module
+------------------------
+
+.. automodule:: ibr_xas.ibr_xas
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ibr_xas
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,20 @@
+Welcome to IBR-XAS's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   installation
+   usage
+   modules
+   contributing
+   authors
+   history
+
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/_sources/installation.rst.txt b/_sources/installation.rst.txt
@@ -0,0 +1,60 @@
+.. highlight:: shell
+
+============
+Installation
+============
+
+
+Stable release
+--------------
+
+(This is currently not available. This will be available after publication)
+
+To install IBR-XAS, run this command in your terminal:
+
+.. code-block:: console
+
+    $ pip install ibr-xas
+
+This is the preferred method to install IBR-XAS, as it will always install the most recent stable release.
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+
+From sources
+------------
+
+The sources for IBR-XAS can be downloaded from the `Github repo`_.
+
+You can install directly with pip:
+
+.. code-block:: console
+
+    $ pip install git+https://github.com/Ameyanagi/IBR-XAS
+
+Or you can download the source code and install it by yourself.
+In order to do so, you can either clone the public repository:
+
+.. code-block:: console
+
+    $ git clone git://github.com/Ameyanagi/IBR-XAS
+
+Or download the `tarball`_:
+
+.. code-block:: console
+
+    $ curl -OJL https://github.com/Ameyanagi/ibr_xas/tarball/master
+
+Once you have a copy of the source, you can install it with:
+
+.. code-block:: console
+
+    $ python setup.py install
+
+
+.. _Github repo: https://github.com/Ameyanagi/IBR-XAS
+.. _tarball: https://github.com/Ameyanagi/IBR-XAS/tarball/master
diff --git a/_sources/modules.rst.txt b/_sources/modules.rst.txt
@@ -0,0 +1,7 @@
+ibr_xas
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   ibr_xas
diff --git a/_sources/readme.rst.txt b/_sources/readme.rst.txt
@@ -0,0 +1 @@
+.. include:: ../README.rst
diff --git a/_sources/usage.rst.txt b/_sources/usage.rst.txt
@@ -0,0 +1,19 @@
+=====
+Usage
+=====
+
+Following is an example usage of the class.
+
+1. Prepare list of energy, and mu. The energy and mu has to be in the format of list of np.ndarray.
+2. Create an instance of the class.
+3. Call the calc_bragg_iter method to iteratively calculate the Bragg peaks.
+4. Call the save_dat method to save the spectra.
+
+         .. code-block:: python
+
+            from ibr_xas import IbrXas
+
+            energy_list, mu_list, file_list = prepare_spectra_from_qas(file_path)
+
+            ix = IbrXas(energy_list, mu_list, file_list)
+            ix.calc_bragg_iter().save_dat()
diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js
@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}