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Add transform images
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rayosborn committed Jan 5, 2024
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25 changes: 20 additions & 5 deletions docs/source/introduction.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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.*
13 changes: 8 additions & 5 deletions docs/source/server.rst
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Expand Up @@ -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:
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