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A. Software Development: Calamari
Calamari is a joint cyber infrastructure product of CIRDLES and GA. As of March 2017, it is a stand-alone Java application that users download and run on their own computers. Calamari reflects progress to date in replicating the mathematics of Ken Ludwig's Excel 2003-based add-in SQUID 2.50. The goal is to demonstrate the efficacy of our work in engineering a replacement for SQUID 2.50.
As of March 2017, Calamari parses Prawn XML data files generated during SHRIMP analytical sessions, and reports if the XML file does not conform to our existing schema. If the XML file does conform, then Calamari will produce a folder of 6 reports in CSV format. Two of these (Check_01… and Check_02…) are ‘checks’ designed to provide key data, harvested from the XML file, as input for manual verification of calculations. The remaining four (SQUID_01… to SQUID_04…) have been designed to replicate key sections of the Excel workbook generated by processing a Prawn Data XML file using SQUID 2.50. The nature and content of these six CSV files are documented below.
In seeking to replicate SQUID 2.50, our initial focus is on its most common use-case, which is single-collector data collected in Counter (i.e. electron multiplier) mode, for the purpose of U-Pb geochronology.
In addition, because we have prioritised emulation of the ‘core’ arithmetic of SQUID 2.50 ahead of its customisable features, Calamari is restricted to the processing of zircon (or baddeleyite) data acquired using one of two ‘classical’ run-tables:
- ‘9-peak zircon’ (comprising species 196 ([90Zr]2 16O), 204 (204Pb), 204.1 (background), 206 (206Pb), 207 (207Pb), 208 (208Pb), 238 (238U), 248 (232Th 16O) and 254 (238U 16O).
- ‘10-peak zircon’, which is the same as 9-peak zircon, but with species 270 (238U [16O]2) added to the high-mass end.
Furthermore, Calamari currently lacks most of the error-trapping built into the corresponding sections of the SQUID VBA code, so it is important that input XML files are ‘well-behaved’ in an analytical sense. For example:
- All analyses within a single XML file need to have the same run-table (i.e. the same set of species, in the same order). Numbers of scans and species counting-times can vary from analysis to analysis, but the identity and analytical sequences of the measured species must not.
- Secondary beam monitor (SBM) data must be present, and must be sensible relative to the analysis-specific SBM_zero value. XML files containing SBM values smaller than the SBM_zero do not trigger error-messages (or automated over-ride of user-preferences for SBM-normalisation, as is the case in SQUID 2.50), they will simply result in negative count-rates for SBM-normalised data.
In order to use Calamari, you will need the following:
- A computer running a 64-bit Operating System (Linux, Mac, Windows)
- Java 1.8 or later
- The latest release of Calamari. You will run the ".jar" file.
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Launch Calamari by double-clicking the ".jar" file. If it won't open, be sure to associate the ".jar" extension with the java runtime. Otherwise, open a terminal window, navigate to the folder with the ".jar" file, type: "java -jar %the name of your calamari jar file%" and press the Return key.
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Click the "Select Prawn XML File" button and you will be given the choice of two example XML files (although you are welcome to try your own Prawn XML file if you believe it conforms to the guidelines above):
- 100142_G6147_10111109.43.xml = 10-peak zircon (mass 196-270, background is third mass-station), also available here: 100142_G6147_10111109.43_original.zip
- GA6030_070322.xml = 9-peak zircon (mass 196-254, background is third mass-station), also available here: GA6030_070322.zip
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The default location for the Reports folder is adjacent to the Calamari ".jar" file.
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Specify the three fundamental user-defined parameters for the earliest stages of data-processing:
- Should ion counts be normalised to SBM counts?
- Should Dodson-interpolated (inter-scan) isotopic ratio be converted into a single analysis-specific isotopic ratio via linear regression to burn mid-time (‘linear regression’), or via time-independent weighted mean (‘spot average’)?
- What is the initial (single) alphanumeric character (case-insensitive) used in labelling analyses of the 206/238 reference zircon/baddeleyite?
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Click the "Reduce Data and Produce Reports" button, and the progress bar will show calculation progress.
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Navigate to the Reports folder and open the CSV files.
Calamari produces six reports (as CSV files) from the selected Prawn XML file, each named using the first eight characters of the XML file followed by an underscore (e.g. '100142_G_'), followed by either 'SBM_' or 'NOSBM_', followed by either 'LINREG_' or 'SPOTAV_', followed by one of the headings (listed below) that begin with either 'Check_' or 'SQUID_'.
As an example, a report from processing the Prawn XML file ‘100142_G6147_10111109.43.xml’ using SBM and SPOTAV parameter choices, yields the filename '100142_G__SBM_SPOTAV_Check_01_IonIntegrations_PerScan.csv'.
All six CSV files are placed inside a folder named '[YYYYMMDD-HH24MISS][X][Y]', where the first part is the system time-stamp for folder creation (unidirectional downward from year to second, and with HH24 = hour in 24-hour format), [X] is either 'SBM' or 'NOSBM', and [Y] is either 'LINREG' or .SPOTAV'.
In turn, this folder is placed inside another folder named the same as the Prawn XML file, without the '.csv' extension.
All report folders are included inside the user's choice of a CalamariReports folder, which defaults to a folder names 'CalamariReports_v[CalamariVersionNumber]', in the same folder as the Calamari '.jar' file that is executing the analysis.