Tools
=====

Various tools are available in SPCal to help with providing sample inputs and manipulating signal data.
These are found in the **Edit** menu.

Density Database
----------------

The **Density Database** is a library containing the :term:`density` for elements [1]_, common inorganic materials [2]_ and polymers [3]_.
The database is searchable using the formula, name or CAS number of a compound.
If started from the :ref:`Isotope Options` dock :term:`density` field, double-clicking a compound or selecting and pressing *Ok* will populate that field with the selected value.

Ionic Response Calculator
-------------------------

.. _ionic response example:
.. figure:: ../images/tools_response_dialog.png
    :align: center

    Measurement of a dissolved standard, the mean of the signal (red line) can be used to determine the :term:`ionic response`.

To calculate the :term:`ionic response` one or more dissolved standards must be run under the same conditions as the spICP-MS sample.
When one standard is used, the :term:`ionic response` is taken as the mean value of the data, :numref:`ionic response example`.
When two or more are used, a calibration curve is created, with the :term:`ionic response` taken as the slope of that curve.

Ideally a blank and several dissolved standards are analysed, covering the range of signal produced by nano-particles in the sample.
In practice, a blank and one standard are usually sufficient.
As the :term:`ionic response` will change day-to-day with instrument conditions so should be determined every run.

The **Ionic Response Calculator** is used to calculate the :term:`ionic response` using one or more data files.
To use the calculator import one or more data files and set their corresponding concentrations in the *Concentrations* table .
For information on importing data see :ref:`Data Import`.

Once all levels are imported the :term:`ionic response` (the calibration slope) and calibrations can be exported using the *Save* button.
After pressing *Ok*, all isotope :term:`ionic response` values will then be added to the processing method and the :ref:`Isotope Options` dock.


Mass Fraction Calculator
------------------------

.. figure:: ../images/tools_mass_fraction.png
   :align: center

   The **Mass Fraction Calculator** calculates the :term:`molar mass` (here MW=215.8 g/mol) and the :term:`mass fraction` from an input formula.
   The element for which the :term:`mass fraction` will be returned is highlight in bold.

This calculator computes the :term:`mass fraction` of the first element from a given formula.
For example, the formula ``FeMoO4`` will give the :term:`mass fraction` for iron and ``MoFeO4`` the :term:`mass fraction` for molybdenum.
When started from the  :term:`mass fraction` field of the :ref:`Isotope Options` dock, the corresponding field will be filled.


.. |c1| unicode:: U+2460
.. |c2| unicode:: U+2461
.. |c3| unicode:: U+2462
.. |c4| unicode:: U+2463
.. |c5| unicode:: U+2464


Signal Calculator
-----------------

Simple arithmetic operations can be performed on signal data using the calculator found at **Edit -> Signal Caluclator**. 
One example is the recovery of sensitivity for multi-isotopic elements, where the total elemental signal is split across multiple masses.
Some of this lost sensitivity can be recovered by summing the individual isotopic signals [4]_.

.. _results calculator:
.. figure:: ../images/tools_signal_calculator.png
   :align: center

   The Signal Calculator can be used to perform arithmetic operations on one or more element.

To start a calculation, enter a mathematical formula in the *Formula* box, using the current element names and the ``+ - ^ * /`` operators.
For example, given data names in the format ``10xAg``, the sum of silver isotopes can be calculated using ``107Ag + 109Ag``.
If no name is given then the default name of the output result will be the parsed expression enclosed by parenthesis, e.g. ``( + 107Ag 109Ag)``.
The result is a new isotope like signal called a :term:`isotope expression`.

.. [1] National Library of Medicine PubChem Periodic Table of Elements. https://pubchem.ncbi.nlm.nih.gov/periodic-table/
.. [2] Kholodovych, V.; Welsh, W. J. Densities of Amorphous and Crystalline Polymers. In Physical Properties of Polymers Handbook; Mark, J. E., Ed.; Springer New York: New York, NY, 2007; pp 611–617. https://doi.org/10.1007/978-0-387-69002-5_37.
.. [3] Yaws, C. L.; Chen, D. H. Density of Solid—Inorganic Compounds. In Thermophysical Properties of Chemicals and Hydrocarbons; Elsevier, 2009; pp 296–308. https://doi.org/10.1016/B978-081551596-8.50011-0.
.. [4] Lockwood, T. E.; Gonzalez De Vega, R.; Du, Z.; Schlatt, L.; Xu, X.; Clases, D. Strategies to Enhance Figures of Merit in ICP-ToF-MS. J. Anal. At. Spectrom. 2024, 39 (1), 227–234. https://doi.org/10.1039/D3JA00288H.