.. _hpMCA:

hpMCA
=====



GUI basics
----------

.. figure:: /images/hpmca/start_file_loaded.png
   :alt: start_file_loaded
   :width: 720px
   :align: center

Left panel (from top to bottom):

- :ref:`Acquisition <acquisition>`
- :ref:`Elapsed time  <elapsed_time>`
- :ref:`Save data file  <save_data_file>`
- :ref:`File saving options <file_save_options>`
- :ref:`Regions of interest <rois>`
- :ref:`Fluorescence markers <fluorescence>`
- :ref:`Vertical scale <v_scale>`
- :ref:`Horizontal scale <h_scale>`

The plot area supports the following mouse commands:

- *Left Click:*
    Move the vertical line cursor to the current mouse position.   

- *Left Drag:*
    Zoom-in to the selected area.

- *Right Click:*
    Zoom out.

- *Mouse Wheel:*
    Zoom in and zoom out centered around the current mouse position.

Bottom panel: Energy and Counts information corresponting to location selected by the cursor

Menu bar: 

* File
   * Open file
   * Open detector
   * Overlay
   * Save as
   * Export pattern
   * Environment
   * Multiple spectra

* Control
   * Calibrate Energy
   * Calibrate 2-theta
   * Set 2-theta
   * Set wavelength
   * Presets

* Display
   * Phase
   * Fluorescence
   * Retions of interest
   * Lattice refinement
   * Colors options
   * ROI options

.. _acquisition:

Acquisition
-----------

- To start data collection, press :guilabel:`&Erase` and then :guilabel:`&On` in 'Acquisition' panel.
- To stop data collection and to save, press :guilabel:`&Off`.

.. _elapsed_time:
 
Elapsed time 
------------
Elapsed time section

.. _save_data_file:

Save data file
--------------
Save data file section

Data files are saved with a ``*.hpmca`` extension.

.. _file_save_options:

File saving options
-------------------

File saving options section



.. _rois:

Regions of Interest (ROI)
-------------------------
There are two methods to add an ROI.

(1)	:ref:`Manual selection of ROI. <manual_roi>`
(2)	:ref:`Make ROI on all peaks for a crystal by using the JCPDS data. <jcpds_roi>`

.. _manual_roi: 

    (1)	**Manual selection of ROI**

        #. Select center of region of interest by moving cursor to that position (Left-click with mouse).
        #. Click, :guilabel:`&Add` button in 'ROIs' panel. The button will now read 'Set'.
        #. Drag left and right extends of the ROI to appropriate positions.

        .. figure:: /images/hpmca/roi_set.png 
           :alt: hpmca_roi_set
           :width: 600px
           :align: center
           
        4. Then, click :guilabel:`&Set` button in 'ROIs' panel. The ROI area should now be a different color (default – blue).
        #. Currently selected ROI is indicated by a red cursor above it.
        #. The Centroid of the selected ROI is displayed in top-middle of the plot.
        #. Different ROI can be selected by :guilabel:`&<` and :guilabel:`&>` buttons in the ROI panel.
        #. More information about the ROIs can be displayed in the 'ROIs control' by selecting menu: Display/ROIs.
        #. You can change the name of any ROI by double-clicking and typing a new name in the name column.
        #. Peak fit can be displayed by clicking 'Show fit' button in ROIs control window.

    .. figure:: /images/hpmca/rois.png
       :alt: rois
       :width: 500px
       :align: center

    .. figure:: /images/hpmca/hpmca_roi_control.png
       :alt: hpmca_roi_control
       :width: 300px
       :align: center

.. _jcpds_roi: 

    (2)	**Make ROIs on all peaks for a crystal by using JCPDS phase**

        #. Open 'Phase control' window from menu \ :menuselection:`Display --> Phase`
        
        .. figure:: /images/hpmca/phase.png
           :alt: phase
           :width: 500px
           :align: center 

        2. Select material by opening a jcpds file.
        #. Check if 2\ :math:`{\theta}` angle is correct, adjust if needed.
        #. Lines, which indicate positions of the peaks of the material, appear below EDXD data.

        .. figure:: /images/hpmca/hpmca_phase_lines.png
           :alt: hpmca_phase_lines
           :width: 500px
           :align: center
        
        5. The positions of peaks lines can be shifted by changing 'P (GPa)', or 'T (K)'.
        
        #. Then, click :guilabel:`&Add ROIS` in 'Phase control' window to add ROIs for all peaks.

To erase a ROI, please click :guilabel:`Delete` after selection of the ROI.
To erase all ROIs, please click :guilabel:`Clear All`.

.. _fluorescence:

Fluorescence markers
--------------------  

By typing in an element, hpMCA shows K and/or L shell emission lines positions.

.. _v_scale:

Vertical scale
-------------------

Vertical scale section

.. _h_scale:

Horizontal scale
----------------

Horizontal scale section

Energy calibration
------------------

Beamline scientist does energy calibration of the germanium solid state detector 
by using Fluorescence lines of silver at 22.104 keV (K\ :math:`{\alpha}`) and 
24.942 keV (K\ :math:`{\alpha}`:sub:`1`), and gammas from 109Cd (88.04 keV) and 57Co (122.10  keV) 
at the beginning of each beamtime cycle.  Parameters of energy calibration (\ :math:`Energy = CAL\_OFFSET + CAL\_SLOPE \cdot Channel`) can 
be found in the header of the EDXD data file.

.. figure:: /images/hpmca/hpmca_file_header.png
   :alt: hpmca_file_header
   :width: 500px
   :align: center

2\ :math:`{\theta}` angle calibration
-------------------------------------
Beamline scientist does 2\ :math:`{\theta}` angle calibration at 7°, 15°, 23°, and 31° 
using unit-cell volume of Au, and make linear equation to calculate 2\ :math:`{\theta}` angle.

The following is the procedure for 2\ :math:`{\theta}` angle calibration:

- Collect Au EDXD pattern.
- :ref:`Make ROIs <jcpds_roi>` for all Au peaks using JCPDS data at 0 GPa.
- Select \ :menuselection:`Control --> Calibrate 2theta…` on Menu bar.
- Please remove weak or overlapping peaks by unchecking them in the column 'Use?'.

.. Note:: Because the MCA does not have background subtraction feature, background slope at low energy (<~25 keV) probably due to absorption influences on determining peak position. It is better not to use low energy data for 2\ :math:`{\theta}` angle calibration. Typically, at 2\ :math:`{\theta}` of ~15 °, the first and second peaks show marked deviation from other peaks.



- Click :guilabel:`Compute 2-theta`.
- 2\ :math:`{\theta}` value appears in the '2\ :math:`{\theta}`' box.
- Then, please click :guilabel:`OK` to apply the 2\ :math:`{\theta}` calibration.

.. figure:: /images/hpmca/hpmca_2theta_calibration.png
   :alt: hpmca_2theta_calibration
   :width: 550px
   :align: center

.. note:: The 2\ :math:`{\theta}` calibration result is also saved in the header of the data file.