documentation added

.gitignore

@@ -2,4 +2,5 @@
 *.csv
 __pycache__/
 *.pyc
-*.pytest_cache/
+*.pytest_cache/
+*.txt

Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Overview.md

@@ -0,0 +1,12 @@
+# Overview
+
+
+Miniaturizing transistors, the building blocks of integrated circuits, presents significant challenges for the semiconductor industry. Precisely measuring these features during production is crucial for high-quality chips. Existing in-line metrology techniques, such as optical critical-dimension (OCD) scatterometry and critical-dimension scanning electron microscopy (CD-SEM), are nearing their limits. OCD struggles with the inherent limitations of light and shrinking features, while CD-SEM, despite providing valuable insights, is restricted by sampling area and resolution. To overcome these obstacles, the industry is exploring X-ray-based metrology. X-rays, with their shorter wavelengths, allow for more precise analysis and are sensitive to variations in composition, providing richer data.
+
+
+CD-SAXS (Critical Dimension Small Angle X-ray Scattering) is a promising technique for nanostructure electronics. It uses a transmission geometry, sending the beam through the sample and the 750 micrometer-thick silicon wafer. The x-ray spot size varies between 10-1000 μm, enabling the measurement of small patterned areas. Studies have shown CD-SAXS's effectiveness in characterizing the shape and spacing of nanometer-sized patterns.
+
+This technique utilizes variable-angle transmission scattering. By rotating the sample, it can probe the vertical profile of the nanostructures, allowing for the reconstruction of their shape and composition in two or even three dimensions. This technique excels at reconstructing intricate shapes smaller than 15 nm and with spacing around 30 nm, dimensions crucial for the semiconductor industry.
+
+Although several big companies are developing software for CD-SAXS, the technique is still in its infancy and there isn't a coherent package available. Thus this cdsaxs package is
+aimed at providing simulation and fitting tools for CD-SAXS synchotron data. It can be separated into two main parts: simulations and fitter. Simulations generate synthetic data for a given model, while the fitter fits the model to the experimental data.  

README.md

@@ -1,3 +1,9 @@
+# Critical Dimension Small Angle X-ray Scattering (cdsaxs) Package
+
+The `cdsaxs` package is a Python package for simulating and fitting cdsaxs data obtained from synchrotron experiments. This package is developed to help researchers extract the
+different parameters of the nanostructures from the experimental data. The collection of functions developed at CEA (French Alternative Energies and Atomic Energy Commission) by former PhD students and at
+Lawrence Berkeley National Laboratory and Brookhaven National Laboratory served as the foundation for this package[[1]](#references).
+
 # Installation
 You can install the package by running the following command in the terminal:
 ```bash
@@ -99,3 +105,6 @@ Then use MCMC method to give you statistics of the best fit.
 ```python
 mcmc = Fitter1.mcmc(N=9, sigma=np.asarray([100] * 9), nsteps=1000, nwalkers=18)
 ```
+
+## References
+1. [Xi-cam cdsaxs repository](https://github.com/Xi-CAM/Xi-cam.CDSAXS/tree/master/xicam/CDSAXS)

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build/html/.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: 9bcbdf391134004e1437a71f8567e779
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_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;
+}