.. _Example-Viewing-LRMECS-Data:

================================================
Viewing 2-D Data from LRMECS
================================================

The IPNS LRMECS instrument stored data in NeXus HDF4 data files.  
One such example is available from the repository of NeXus data 
file examples.
For this example, we will start with a conversion of that 
original data file into *HDF5* format.

	:HDF4:
		http://svn.nexusformat.org/definitions/exampledata/IPNS/LRMECS/lrcs3701.nxs
	:HDF5:
		http://svn.nexusformat.org/definitions/exampledata/IPNS/LRMECS/lrcs3701.nx5

This dataset contains two histograms with 2-D images (148x750 and 148x32) of 32-bit integers.
First, we use the ``h5dump`` tool to investigate the header content of the file 
(not showing any of the data).


Visualize Using ``h5dump``
###############################

Here, the output of the command::

	h5dump -H lrcs3701.nx5

has been edited to only show the first *NXdata* group (``/Histogram1/data``):

LRMECS ``lrcs3701`` data: ``h5dump`` output
++++++++++++++++++++++++++++++++++++++++++++++++++

.. literalinclude:: dump-histogram1-data.txt
    :tab-width: 4
    :linenos:
    :language: guess


Visualize Using *HDFview*
###############################

For many, the simplest way to view the data content 
of an HDF5 file is to use the  *HDFview* program 
(http://www.hdfgroup.org/hdf-java-html/hdfview)
from The HDF Group.  After starting *HDFview*, the data file 
may be loaded by dragging it into the main HDF window.
On opening up to the first ``NXdata`` group */Histogram1/data*
(as above), and then double-clicking the dataset called: *data*, we get
our first view of the data.

.. figure:: hdfview.jpg
    :alt: fig.data-linking
    :width: 80%

    LRMECS ``lrcs3701`` data: *HDFview*

The data may be represented as an image by accessing the *Open As*
menu from HDFview (on Windows, right click the dataset called *data*
and select the *Open As* item, consult the HDFview documentation 
for different platform instructions).  Be sure to select the *Image* 
radio button, and then (accepting everything else as a default) press the
*Ok* button.

.. note:: In this image, dark represents low intensity 
			while white represents high intensity.

.. figure:: hdfview-open-as.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *HDFview* *Open As* dialog

LRMECS ``lrcs3701`` data: image
++++++++++++++++++++++++++++++++++++++++++++++++++

.. figure:: hdfview-image.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *HDFview* Image


Visualize Using *IgorPro*
###############################

Another way to visualize this data is to use a commercial 
package for scientific data visualization and analysis.  
One such package is *IgorPro* from http://www.wavemetrics.com

IgorPro provides a browser for HDF5 files that can open our 
NeXus HDF5 and display the image.  Follow the instructions 
from WaveMetrics to install the *HDF5 Browser* package:  
http://www.wavemetrics.com/products/igorpro/dataaccess/hdf5.htm

You may not have to do this step if you have already installed the *HDF5 Browser*.
IgorPro will tell you if it is not installed properly.
To install the *HDF5 Browser*, first start *IgorPro*.
Next, select from the menus and submenus: 
``Data; Load Waves; Packages; Install HDF5 Package`` as shown in the next figure.
IgorPro may direct you to perform more activities before you progress from this step.

.. figure:: igor-install-hdf5-package.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *IgorPro* install HDF5 Browser

Next, open the *HDF5 Browser* by selecting from 
the menus and submenus:  
``Data; Load Waves; New HDF5 Browser`` 
as shown in the next figure.

.. figure:: igor-menu-selection.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *IgorPro* *HDFBrowser* dialog

Next, click the *Open HDF5 File* button and 
open the NeXus HDF5 file ``lrcs3701.nxs``.  In the lower left *Groups*
panel, click the *data* dataset.  Also, under the panel
on the right called *Load Dataset Options*,
choose ``No Table`` as shown.  Finally, click the 
*Load Dataset* button (in the *Datasets* group) 
to display the image.

.. note:: In this image, dark represents low intensity 
	      while white represents high intensity.  The image has 
	      been rotated for easier representation in this manual.

.. figure:: Igor-HDFBrowser-demo.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *IgorPro* *HDFBrowser* dialog

LRMECS ``lrcs3701`` data: image
++++++++++++++++++++++++++++++++++++++++++++++++++

.. figure:: igor-data.jpg
    :width: 80%

    LRMECS ``lrcs3701`` data: *IgorPro* Image