Adds more documentation, sample scaling in the point picking dialog, …

…replaces BitMask with bitarray, and makes icons lighter.
ISISNeutronMuon · Oct 25, 2019 · 24427bc · 24427bc
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diff --git a/README.md b/README.md
@@ -16,6 +16,7 @@ This will be moved to requirements.txt later
   * PyOpengl
   * NLopt
   * pystache
+  * Sphinx (optional)
   * coverage (optional)
   * PyInstaller (optional)
 
@@ -26,10 +27,21 @@ When the first release is complete, an installer will be provided but this infor
 
 1. Download the repository 
 2. Add the following line in **main.py** after the ``import sys`` statement  
-    ``sys.path.append('path to the SScanSS-2 folder')``
+
+        sys.path.append('path to the SScanSS-2 folder')
 3. Open a terminal and navigate to the **SScanSS-2** directory then  
-    ``cd sscanss``  
-    ``python main.py`` 
+
+        cd sscanss
+        python main.py
+
+How to build the documentation
+------------------------------
+The documentation currently hosted using Github pages at [https://isisneutronmuon.github.io/SScanSS-2/](https://isisneutronmuon.github.io/SScanSS-2/).
+The source is in **docsrc** folder while the build is in the **docs** folder. Source can be  built using Sphinx make file.
+
+    cd docsrc
+    make github
+
 
 Citing SScanSS 2
 ----------------

diff --git a/docs/_images/add_fiducials.png b/docs/_images/add_fiducials.png
diff --git a/docs/_images/add_measurements.png b/docs/_images/add_measurements.png
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diff --git a/docs/_images/another_model.png b/docs/_images/another_model.png
diff --git a/docs/_images/arrow.png b/docs/_images/arrow.png
diff --git a/docs/_images/camera.png b/docs/_images/camera.png
diff --git a/docs/_images/cross.png b/docs/_images/cross.png
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diff --git a/docs/_images/insert_primitive.png b/docs/_images/insert_primitive.png
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diff --git a/docs/_images/limit.png b/docs/_images/limit.png
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diff --git a/docs/_images/origin.png b/docs/_images/origin.png
diff --git a/docs/_images/plane_align.png b/docs/_images/plane_align.png
diff --git a/docs/_images/plane_alignment.png b/docs/_images/plane_alignment.png
diff --git a/docs/_images/point.png b/docs/_images/point.png
diff --git a/docs/_images/point_from_graphics.png b/docs/_images/point_from_graphics.png
diff --git a/docs/_images/point_manager.png b/docs/_images/point_manager.png
diff --git a/docs/_images/positioners.png b/docs/_images/positioners.png
diff --git a/docs/_images/preferences.png b/docs/_images/preferences.png
diff --git a/docs/_images/redo.png b/docs/_images/redo.png
diff --git a/docs/_images/rotate.png b/docs/_images/rotate.png
diff --git a/docs/_images/rotate_sample.png b/docs/_images/rotate_sample.png
diff --git a/docs/_images/sample_manager.png b/docs/_images/sample_manager.png
diff --git a/docs/_images/save.png b/docs/_images/save.png
diff --git a/docs/_images/select.png b/docs/_images/select.png
diff --git a/docs/_images/start.png b/docs/_images/start.png
diff --git a/docs/_images/transform-matrix.png b/docs/_images/transform-matrix.png
diff --git a/docs/_images/transform_sample.png b/docs/_images/transform_sample.png
diff --git a/docs/_images/translate.png b/docs/_images/translate.png
diff --git a/docs/_images/translate_sample.png b/docs/_images/translate_sample.png
diff --git a/docs/_images/undo.png b/docs/_images/undo.png
diff --git a/docs/_images/vector_manager.png b/docs/_images/vector_manager.png
diff --git a/docs/_static/banner.png b/docs/_static/banner.png
diff --git a/docs/_static/bootstrap-sphinx.css b/docs/_static/bootstrap-sphinx.css
@@ -18,7 +18,7 @@
 
 
 
-    @import url("./bootswatch-3.3.7/simplex/bootstrap.min.css");
+    @import url("./bootswatch-3.3.7/lumen/bootstrap.min.css");
 
 
 

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: '',
-    VERSION: '0.0.1-alpha',
+    VERSION: '1.0.0-beta',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/_static/style.css b/docs/_static/style.css
@@ -0,0 +1,9 @@
+body { line-height: 1.8 !important; }
+
+h1 { font-size: 40px !important; }
+h2 { font-size: 32px !important; }
+h3 { font-size: 24px !important; }
+h4 { font-size: 18px !important; }
+h5 { font-size: 14px !important; }
+h6 { font-size: 10px !important; }
+code { color: #158cba !important; }
diff --git a/docs/add_fiducials.html b/docs/add_fiducials.html
@@ -4,18 +4,17 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Insert Fiducial Points &#8212; SScanSS 2 0.0.1-alpha documentation</title>
+    <title>Insert Fiducial Points &#8212; SScanSS 2 1.0.0-beta documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <link rel="stylesheet" href="_static/style.css" type="text/css" />
     <script type="text/javascript" src="_static/documentation_options.js"></script>
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Insert Measurement Points" href="add_measurements.html" />
-    <link rel="prev" title="Transform Sample" href="transform_sample.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -38,12 +37,16 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.0.1-alpha</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
           <ul class="nav navbar-nav">
 
+                <li><a href="api.html">API</a></li>
+                <li><a href="tutorials.html">Tutorials</a></li>
+                <li><a href="guides.html">User Guide</a></li>
+
 
               <li class="dropdown globaltoc-container">
   <a role="button"
@@ -53,23 +56,7 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"><ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="overview.html">General Overview</a></li>
-<li class="toctree-l1"><a class="reference internal" href="example.html">Example Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_sample.html">Insert Sample</a></li>
-<li class="toctree-l1"><a class="reference internal" href="transform_sample.html">Transform Sample</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Insert Fiducial Points</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_measurements.html">Insert Measurement Points</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_vectors.html">Insert Measurement Vectors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="configure_instrument.html">Instrument Configuration</a></li>
-<li class="toctree-l1"><a class="reference internal" href="align_sample.html">Align Sample on Instrument</a></li>
-<li class="toctree-l1"><a class="reference internal" href="simulation.html">Simulating Experiments</a></li>
-</ul>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="api.html">API Reference</a></li>
-<li class="toctree-l1"><a class="reference internal" href="api.html#indices-and-tables">Indices and tables</a></li>
-</ul>
-</ul>
+      aria-labelledby="dLabelGlobalToc"></ul>
 </li>
 
                 <li class="dropdown">
@@ -82,7 +69,7 @@
       role="menu"
       aria-labelledby="dLabelLocalToc"><ul>
 <li><a class="reference internal" href="#">Insert Fiducial Points</a><ul>
-<li><a class="reference internal" href="#loading-a-fiducial-fiducial-file">Loading a fiducial (.fiducial) file</a></li>
+<li><a class="reference internal" href="#loading-fiducial-points-from-file">Loading fiducial points from file</a></li>
 <li><a class="reference internal" href="#key-in-fiducial-points">Key-in fiducial points</a></li>
 <li><a class="reference internal" href="#manage-fiducial-points">Manage fiducial points</a><ul>
 <li><a class="reference internal" href="#edit-fiducial-points">Edit fiducial points</a></li>
@@ -127,27 +114,33 @@
   <div class="section" id="insert-fiducial-points">
 <h1>Insert Fiducial Points<a class="headerlink" href="#insert-fiducial-points" title="Permalink to this headline">¶</a></h1>
 <p>Fiducial points are used in SScanSS to determine the position and orientation of a sample after it has been moved to
-instrument.</p>
-<div class="section" id="loading-a-fiducial-fiducial-file">
-<h2>Loading a fiducial (.fiducial) file<a class="headerlink" href="#loading-a-fiducial-fiducial-file" title="Permalink to this headline">¶</a></h2>
-<p>The fiducial points may be imported from comma or space delimited file. The file must contain three columns representing the
-fiducial point and an optional fourth row which specifies enabled status (more on this later). To import .fiducial files, Go to
-<strong>Insert &gt; Fiducial Points &gt; File…</strong>,  browse to the location of the file and select it. The fiducial points will be rendered
+instrument. The fiducial points will be rendered
 as spheres in the graphics window.</p>
+<div class="section" id="loading-fiducial-points-from-file">
+<h2>Loading fiducial points from file<a class="headerlink" href="#loading-fiducial-points-from-file" title="Permalink to this headline">¶</a></h2>
+<p>To import a <a class="reference internal" href="file_types.html#fiducial-file"><span class="std std-ref">Fiducial point file (.fiducial)</span></a>, Go to <strong>Insert &gt; Fiducial Points &gt; File…</strong>,  browse to the location of the file and
+select it.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">Imported points will not replace existing points but will be appended to them. Delete old points from
+point manager if necessary.</p>
+</div>
 </div>
 <div class="section" id="key-in-fiducial-points">
 <h2>Key-in fiducial points<a class="headerlink" href="#key-in-fiducial-points" title="Permalink to this headline">¶</a></h2>
 <p>Click <strong>Insert &gt; Fiducial Points &gt; Key-In</strong> and  type in the X, Y, and Z values of the fiducial points and click <strong>Add Fiducial Point</strong>
 button. The fiducial point should be displayed in the graphics window</p>
+<a class="reference internal image-reference" href="_images/add_fiducials.png"><img alt="Key-in Fiducials Window" class="align-center" src="_images/add_fiducials.png" style="width: 404.8px; height: 266.40000000000003px;" /></a>
 </div>
 <div class="section" id="manage-fiducial-points">
-<h2>Manage fiducial points<a class="headerlink" href="#manage-fiducial-points" title="Permalink to this headline">¶</a></h2>
+<span id="manage-fiducial"></span><h2>Manage fiducial points<a class="headerlink" href="#manage-fiducial-points" title="Permalink to this headline">¶</a></h2>
 <p>Fiducial points can be viewed and managed via the point manager. The point manager will be opened when fiducial points are
 added, if the point manager is closed it can be opened by selecting <strong>View &gt; Other Windows &gt; Fiducial Points</strong> in the menu.
 Points can be edited, re-ordered, deleted, enabled or disabled from the manager, and these operation can be undone (Ctrl+Z)
 if needed. The point manager displays the X, Y, Z coordinate of the point and the enabled status in a table. Selecting a
 point from the manager will cause the corresponding 3D model to be highlighted in the graphics window, this can be useful
 when attempting to identify specific points.</p>
+<a class="reference internal image-reference" href="_images/point_manager.png"><img alt="Point Manager Window" class="align-center" src="_images/point_manager.png" style="width: 405.6px; height: 287.2px;" /></a>
 <div class="section" id="edit-fiducial-points">
 <h3>Edit fiducial points<a class="headerlink" href="#edit-fiducial-points" title="Permalink to this headline">¶</a></h3>
 <p>Double click a table cell, type in the new value and press the Enter key to accept the change</p>
@@ -162,6 +155,8 @@ <h3>Delete fiducial points<a class="headerlink" href="#delete-fiducial-points" t
 </div>
 <div class="section" id="enable-disable-fiducial-points">
 <h3>Enable/Disable fiducial points<a class="headerlink" href="#enable-disable-fiducial-points" title="Permalink to this headline">¶</a></h3>
+<p>Click the check box in the fourth column of the desired point to enable or disable it. Click the check box in the fourth
+column header to enable or disable all points</p>
 </div>
 </div>
 </div>

diff --git a/docs/add_measurements.html b/docs/add_measurements.html
@@ -4,18 +4,17 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Insert Measurement Points &#8212; SScanSS 2 0.0.1-alpha documentation</title>
+    <title>Insert Measurement Points &#8212; SScanSS 2 1.0.0-beta documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <link rel="stylesheet" href="_static/style.css" type="text/css" />
     <script type="text/javascript" src="_static/documentation_options.js"></script>
     <script type="text/javascript" src="_static/jquery.js"></script>
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Insert Measurement Vectors" href="add_vectors.html" />
-    <link rel="prev" title="Insert Fiducial Points" href="add_fiducials.html" />
 <meta charset='utf-8'>
 <meta http-equiv='X-UA-Compatible' content='IE=edge,chrome=1'>
 <meta name='viewport' content='width=device-width, initial-scale=1.0, maximum-scale=1'>
@@ -38,12 +37,16 @@
         </button>
         <a class="navbar-brand" href="index.html">
           SScanSS 2</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.0.1-alpha</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>1.0.0-beta</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
           <ul class="nav navbar-nav">
 
+                <li><a href="api.html">API</a></li>
+                <li><a href="tutorials.html">Tutorials</a></li>
+                <li><a href="guides.html">User Guide</a></li>
+
 
               <li class="dropdown globaltoc-container">
   <a role="button"
@@ -53,23 +56,7 @@
      href="index.html">Site <b class="caret"></b></a>
   <ul class="dropdown-menu globaltoc"
       role="menu"
-      aria-labelledby="dLabelGlobalToc"><ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="overview.html">General Overview</a></li>
-<li class="toctree-l1"><a class="reference internal" href="example.html">Example Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_sample.html">Insert Sample</a></li>
-<li class="toctree-l1"><a class="reference internal" href="transform_sample.html">Transform Sample</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_fiducials.html">Insert Fiducial Points</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">Insert Measurement Points</a></li>
-<li class="toctree-l1"><a class="reference internal" href="add_vectors.html">Insert Measurement Vectors</a></li>
-<li class="toctree-l1"><a class="reference internal" href="configure_instrument.html">Instrument Configuration</a></li>
-<li class="toctree-l1"><a class="reference internal" href="align_sample.html">Align Sample on Instrument</a></li>
-<li class="toctree-l1"><a class="reference internal" href="simulation.html">Simulating Experiments</a></li>
-</ul>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="api.html">API Reference</a></li>
-<li class="toctree-l1"><a class="reference internal" href="api.html#indices-and-tables">Indices and tables</a></li>
-</ul>
-</ul>
+      aria-labelledby="dLabelGlobalToc"></ul>
 </li>
 
                 <li class="dropdown">
@@ -82,7 +69,7 @@
       role="menu"
       aria-labelledby="dLabelLocalToc"><ul>
 <li><a class="reference internal" href="#">Insert Measurement Points</a><ul>
-<li><a class="reference internal" href="#loading-a-measurement-measurement-file">Loading a measurement (.measurement) file</a></li>
+<li><a class="reference internal" href="#loading-measurement-points-from-file">Loading measurement points from file</a></li>
 <li><a class="reference internal" href="#key-in-measurement-points">Key-in measurement points</a></li>
 <li><a class="reference internal" href="#graphical-selection-of-measurement-point">Graphical selection of measurement point</a></li>
 <li><a class="reference internal" href="#manage-measurement-points">Manage measurement points</a></li>
@@ -121,25 +108,40 @@
 
   <div class="section" id="insert-measurement-points">
 <h1>Insert Measurement Points<a class="headerlink" href="#insert-measurement-points" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="loading-a-measurement-measurement-file">
-<h2>Loading a measurement (.measurement) file<a class="headerlink" href="#loading-a-measurement-measurement-file" title="Permalink to this headline">¶</a></h2>
-<p>The measurement points may be imported from comma or space delimited file. The file must contain three columns representing the
-measurement point and an optional fourth row which specifies enabled status (more on this later). To import .measurement files, Go to
-<strong>Insert &gt; Measurement Points &gt; File…</strong>, browse to the location of the file and select it. The measurement points will be rendered
-as stars in the graphics window.</p>
+<p>Measurement points may be imported from a file, typed in, or selected graphically. The measurement points are
+rendered as stars in the graphics window.</p>
+<div class="section" id="loading-measurement-points-from-file">
+<h2>Loading measurement points from file<a class="headerlink" href="#loading-measurement-points-from-file" title="Permalink to this headline">¶</a></h2>
+<p>To import a <a class="reference internal" href="file_types.html#measurement-file"><span class="std std-ref">Measurement file (.measurement)</span></a>, Go to <strong>Insert &gt; Measurement Points &gt; File…</strong>, browse to the location of the file and
+select it.</p>
 </div>
 <div class="section" id="key-in-measurement-points">
 <h2>Key-in measurement points<a class="headerlink" href="#key-in-measurement-points" title="Permalink to this headline">¶</a></h2>
 <p>Click <strong>Insert &gt; Measurement Points &gt; Key-In</strong> and  type in the X, Y, and Z values of the measurement points and click <strong>Add Fiducial Point</strong>
 button. The measurement point should be displayed in the graphics window</p>
+<a class="reference internal image-reference" href="_images/add_measurements.png"><img alt="Key-in Fiducials Window" class="align-center" src="_images/add_measurements.png" style="width: 404.0px; height: 266.40000000000003px;" /></a>
 </div>
 <div class="section" id="graphical-selection-of-measurement-point">
 <h2>Graphical selection of measurement point<a class="headerlink" href="#graphical-selection-of-measurement-point" title="Permalink to this headline">¶</a></h2>
-<p>Click <strong>Insert &gt; Measurement Points &gt; Graphical Selection</strong></p>
+<p>To graphically add measurement point, click <strong>Insert &gt; Measurement Points &gt; Graphical Selection</strong>.</p>
+<a class="reference internal image-reference" href="_images/point_from_graphics.png"><img alt="Graphical selection Window" class="align-center" src="_images/point_from_graphics.png" style="width: 540.0px; height: 752.8000000000001px;" /></a>
+<ul class="simple">
+<li>Adjust plane direction and distance from origin to change cross-section.</li>
+<li>Click the <strong>Selection Tools</strong> tab, and click on the <a class="reference internal" href="_images/point.png"><img alt="point" src="_images/point.png" style="width: 25.6px; height: 25.6px;" /></a> tool.</li>
+<li>Click on the cross-section graphics window to specify point locations.</li>
+<li>Click <strong>Add Points</strong> to selected points to project.</li>
+</ul>
+<p>To delete point:</p>
+<ul class="simple">
+<li>Click the <strong>Selection Tools</strong> tab, and click on the <a class="reference internal" href="_images/select.png"><img alt="select" src="_images/select.png" style="width: 25.6px; height: 25.6px;" /></a> tool.</li>
+<li>Select the points on cross-section graphics window and press the delete key.</li>
+</ul>
 </div>
 <div class="section" id="manage-measurement-points">
 <h2>Manage measurement points<a class="headerlink" href="#manage-measurement-points" title="Permalink to this headline">¶</a></h2>
-<p>similar to fiducial points</p>
+<p>Measurement points can be viewed and managed via the point manager. The point manager will be opened when measurement points are
+added, if the point manager is closed it can be opened by selecting <strong>View &gt; Other Windows &gt; Measurement Points</strong> in the menu.
+Operations for measurement points are similar to <a class="reference internal" href="add_fiducials.html#manage-fiducial"><span class="std std-ref">Manage fiducial points</span></a>.</p>
 </div>
 </div>
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		@import url("./bootswatch-3.3.7/simplex/bootstrap.min.css");
		@import url("./bootswatch-3.3.7/lumen/bootstrap.min.css");



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