deploy: 81e759e

_sources/introduction.rst.txt

@@ -217,8 +217,23 @@ Coordinate Transformation Workflow* (*CCTW*), written by Guy Jennings
 *CCTW* needs to be built from the source code, which is available on
 `SourceForge <https://sourceforge.net/projects/cctw/>`_. *NXRefine*
 generates the parameter file used by *CCTW* for each set of Φ-rotations
-launches the application, and links to the results. Once all the
-rotation scans are processed, they are merged into a single reciprocal
-space grid. On a multi-core system, it is possible to accomplish the
-complete transformation process in less time than it takes to collect
-the data, even though the raw data can exceed 100 GB in size.
+launches the application, and links to the results. 
+
+.. figure:: /images/rotation-transforms.png
+   :align: center
+   :width: 100%
+
+   *CCTW transforms from three rotation scans with detector
+   translations.* 
+
+Once all the rotation scans are processed, they are merged into a single
+reciprocal space grid. On a multi-core system, it is possible to
+accomplish the complete transformation process in less time than it
+takes to collect the data, even though the raw data can exceed 100 GB in
+size.
+
+.. figure:: /images/merged-transform.png
+   :align: center
+   :width: 100%
+
+   *CCTW transform after merging the three rotation scans.* 

_sources/server.rst.txt

@@ -3,15 +3,18 @@ Server Configuration
 *NXRefine* implements a data reduction workflow, which can be run as a
 series of line commands in the terminal. However, since some of the
 processes can take a long time to complete (from a few minutes to an
-hour, depending on the system being used), it is possible to queue these
-operations using the *NXRefine*'s queue manager, to be run locally using multiple cores or distributed to other nodes. The *NXRefine* queue manager can be configured to submit jobs to another job queue manager if one is available. 
+hour, depending on the process and system being used), it is possible to
+queue these operations using the *NXRefine*'s queue manager, to be run
+locally using multiple cores or distributed to other nodes. The
+*NXRefine* queue manager can be configured to submit jobs to another job
+queue manager if one is available. 
 
 Initial Setup
 -------------
 In order to allow *NXRefine* to be used on machines with multiple users,
-a directory is defined to store log files, task queues, and settings,
-which define how the queue is configured and log the results. However,
-if *NXRefine* is installed for use by a single user, this directory can
+a common directory is defined to store log files, task queues, and
+settings, which define how the queue is configured and log the results.
+If *NXRefine* is installed for use by a single user, this directory can
 be in their local home directory.
 
 The location of the server directory needs to be initialized on the command line by the 'nxserver' command:

introduction.html

@@ -238,11 +238,21 @@ <h2>Coordinate Transformation<a class="headerlink" href="#coordinate-transformat
 <p><em>CCTW</em> needs to be built from the source code, which is available on
 <a class="reference external" href="https://sourceforge.net/projects/cctw/">SourceForge</a>. <em>NXRefine</em>
 generates the parameter file used by <em>CCTW</em> for each set of Φ-rotations
-launches the application, and links to the results. Once all the
-rotation scans are processed, they are merged into a single reciprocal
-space grid. On a multi-core system, it is possible to accomplish the
-complete transformation process in less time than it takes to collect
-the data, even though the raw data can exceed 100 GB in size.</p>
+launches the application, and links to the results.</p>
+<div class="figure align-center" id="id2">
+<a class="reference internal image-reference" href="_images/rotation-transforms.png"><img alt="_images/rotation-transforms.png" src="_images/rotation-transforms.png" style="width: 100%;" /></a>
+<p class="caption"><span class="caption-text"><em>CCTW transforms from three rotation scans with detector
+translations.</em></span><a class="headerlink" href="#id2" title="Permalink to this image">¶</a></p>
+</div>
+<p>Once all the rotation scans are processed, they are merged into a single
+reciprocal space grid. On a multi-core system, it is possible to
+accomplish the complete transformation process in less time than it
+takes to collect the data, even though the raw data can exceed 100 GB in
+size.</p>
+<div class="figure align-center" id="id3">
+<a class="reference internal image-reference" href="_images/merged-transform.png"><img alt="_images/merged-transform.png" src="_images/merged-transform.png" style="width: 100%;" /></a>
+<p class="caption"><span class="caption-text"><em>CCTW transform after merging the three rotation scans.</em></span><a class="headerlink" href="#id3" title="Permalink to this image">¶</a></p>
+</div>
 </div>
 </div>
 

server.html

@@ -45,14 +45,17 @@ <h1>Server Configuration<a class="headerlink" href="#server-configuration" title
 <p><em>NXRefine</em> implements a data reduction workflow, which can be run as a
 series of line commands in the terminal. However, since some of the
 processes can take a long time to complete (from a few minutes to an
-hour, depending on the system being used), it is possible to queue these
-operations using the <em>NXRefine</em>’s queue manager, to be run locally using multiple cores or distributed to other nodes. The <em>NXRefine</em> queue manager can be configured to submit jobs to another job queue manager if one is available.</p>
+hour, depending on the process and system being used), it is possible to
+queue these operations using the <em>NXRefine</em>’s queue manager, to be run
+locally using multiple cores or distributed to other nodes. The
+<em>NXRefine</em> queue manager can be configured to submit jobs to another job
+queue manager if one is available.</p>
 <div class="section" id="initial-setup">
 <h2>Initial Setup<a class="headerlink" href="#initial-setup" title="Permalink to this headline">¶</a></h2>
 <p>In order to allow <em>NXRefine</em> to be used on machines with multiple users,
-a directory is defined to store log files, task queues, and settings,
-which define how the queue is configured and log the results. However,
-if <em>NXRefine</em> is installed for use by a single user, this directory can
+a common directory is defined to store log files, task queues, and
+settings, which define how the queue is configured and log the results.
+If <em>NXRefine</em> is installed for use by a single user, this directory can
 be in their local home directory.</p>
 <p>The location of the server directory needs to be initialized on the command line by the ‘nxserver’ command:</p>
 <blockquote>