.. _mapviewer_app:

==========================
GSECARS Mapviewr
==========================

.. _wxmplot:  https://newville.github.io/wxmplot
.. _matplotlib: https://matplotlib.org/


The GSECARS Mapviewer is one of the main GUI applications of Larch,
allowing users to read and display HDF5 files containing X-ray fluorescence
maps from synchrotron X-ray microprobes.  The program plays the dual role
of displaying existing X-ray microprobe maps in HDF5 format and assembling
those HDF5 X-ray microprobe map files from the raw data as collected APS
beamline 13-ID-E or other microprobes using the same Epics scanning
software used there.



.. image:: _images/Mapviewer_1ROI.png
    :target: _images/Mapviewer_1ROI.png
    :width: 50%
.. image:: _images/MapviewerImage_1ROI.png
    :target: _images/MapviewerImage_1ROI.png
    :width: 40%

The Application itself contains two main panels.  On the left is a browser
from which the user can select which of several open map files to use.  On
the right a set of tabbed windows selects how to interact with that
selected map file.

In the first (left most and default) of these tabbed views, one can select
pre-calculated Regions of Interest (ROIs) for viewing.  These ROIs usually
representing a single X-ray fluorescence line for a single element.  One
can view these ROI data as intensity mapse, either shown as a false-color
image for a single ROI, a Red-Green-Blue image for 3 different ROIs, or as
a 2-D grid of maps and correlation plots for 2 different ROIs.

All these images are made using `wxmplot`_ and `matplotlib`_, and are fully
interactive with zooming, changing interpolation methods and color tables,
and setting intensity thresholds.

The images have 3 different "cursor modes" to change how the program
responds to the cursor (left mouse button).  The main mode is that
Left-Mouse-Button down-and-drag draws a rectangle to select a zoomed-in
portion of the image when the button is released.

The user can also put the cursor into a mode to "Pick Area for XRF
Spectrum".  In this mode, the mouse is used to draw freestyle "lasso box"
around any selected points in the map.  When released, the full X-ray
fluorescence spectrum from that map area is extracted from the map and
displays, as shown below.

.. image:: _images/XRFDisplay.png
    :target: _images/XRFDisplay.png
    :width: 75%


.. image:: _images/MapviewerImage_3ROI.png
    :target: _images/MapviewerImage_3ROI.png
    :width: 45%
.. image:: _images/Mapviewer_correlation_maps.png
    :target: _images/Mapviewer_correlation_maps.png
    :width: 45%

Other displays of the same XRF Map data.  On the left, 3 different elements are
encoded into Red, Green, and Blue. On the right, an interactive display of
the correlation of two maps is shown.

.. image:: _images/Mapviewer_XRD_Display.png
    :target: _images/Mapviewer_XRD_Display.png
    :width: 75%

Larch can also handle micro-X-ray Diffraction maps, with a simple view of a
diffraction pattern shown here.
