The Tools
=========

.. _saxsdog:

The Saxsdog
~~~~~~~~~~~

The saxsdog is a script that converts directories with images to curves. It can use multiple threads and watch the file system for changes.
  
For help on the usage type:

.. command-output:: saxsdog --help 
  
The calibration file must be a valid :ref:`root`
 
.. _converter:

The Converter
~~~~~~~~~~~~~


The converter extracts information from the calibration.txt generated by fit2d and adds them to a SAXS.calibration configuration file. (:ref:`root`)
 
.. command-output:: saxsconverter  --help

If there is a  target file and it is a valid :ref:`root`, the parsed values are added or updated in place.

.. _plotchi:

Plotchi
~~~~~~~

The tool "plotchi"  plots a list of ".chi"-files:

.. command-output:: plotchi  --help 

.. _saxsdmerge:

Saxsdmerge
~~~~~~~~~~

This tool adresses a very specific problem only applicable under our beamlines needs.

.. command-output:: saxsdmerge   --help 

What it does is the following: It merges the two log files by interpolating the missing data in the joined table of the the 1 sec interval data logger and the shutter log. The interpolation method takes the closest previous entry. The two logfiles are presumed to have the same clock. This data is then merged with the data extracted from the image headers and dedector logs and is written to a output file as a Table. As the image time stamps are from a different clock which might have a significant offset, the ``-1`` and ``-t`` options allow for dealing with that. In order to check if the time synchronization is reasonable, the tool displays a graph with the shutter times and the exposure times from the images.

One of the output file format options is hdf, the hirarchical data format, which ia a way to create portable binary data files. If you specify hdf, the radial average function "``.chi``" and even the image data  can be written to the hdf file. The hdf export is done with pandas hdf exporter which in turn uses `PyTables <http://www.pytables.org/>`_. The "``.chi``" files reside under the "Graphs" Label, the log data under the "LogData" label and the images if present under the "Images" Label. It can be restored to a Pandas pannel or data frame with:

.. code::

   import pandas as pd
   store=pd.HDFStore("/home/chm/saxs/merged.hdf")
   Curves=store["Curves"] # gives Pandas panel with all the curves
   Data=store["Data"] # gives Pandas data frame of merged log and image parameters