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C. Step 1: Transform XML

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sbodorkos edited this page Mar 20, 2017 · 4 revisions

Step 1: Transform XML into condensed and reformatted 'total counts at peak' worksheet

The first stage of data reduction visible to SQUID users is the transformation of the XML file into ‘condensed and reformatted’ analysis-specific arrays of "total counts at peak" values. For each analysis in a SQUID-book, this array has Nscans rows, and comprises 5 columns per species:

  1. time_stamp_sec at peak (harvested directly from XML)
  2. total ion counts at peak (calculated below)
  3. +/-1sigma value for total ion counts at peak (calculated below)
  4. total SBM counts at peak (calculated below)
  5. trim_mass at peak (harvested directly from XML)

In a SQUID-book, these arrays are presented in a worksheet with a name very similar to that of the source XML file, and at the right-hand end of each array are analysis-specific parameters harvested from the XML file, some of which (e.g. deadtime, sbm_zero) are used in early-stage calculations.

In brief, moving from the parsed XML file to this worksheet involves determining (on a peak by peak basis) for each set of 10 constituent integrations:

  1. a robust mean value for SBM counts, and
  2. a mean (either robust or arithmetic, depending principally on count-rate) and +/- 1sigma value for species-specific counts, incorporating a correction for deadtime in the ion counter (i.e. electron multiplier).

These calculations (which commence with the Preliminary calculations described above) are documented in detail here.

Calamari CSV (SQUID_01…)

In Calamari, these calculations culminate in the Calamari CSV file ‘SQUID_01…”, which is an array matching as closely as possible the ‘condensed PD/XML’ worksheet of a SQUID-workbook (which usually takes the name of the machine-data file created by the SHRIMP control software). The CSV has one row per scan, and 5 columns per species (one for each key attribute of ‘total counts at peak’, as described in detail here).

Value-by-value comparisons of the Step 1 outputs from SQUID 2.50 and Calamari for a specified demonstration XML file are documented at G. Synthesis of Steps 1–4: Cell-by-cell comparisons of SQUID 2.50 and Calamari output.

Next: D. Step 2: Background- and SBM zero-corrections, and 'total CPS' columns

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