Config

{ 
  // Description of intended use of the file, e.g. spike and standard 
  // lot numbers could be annotated here, as well as where and when 
  // spike and standard were calibrated.
  // It's reccomended that creator info/contact is added as well.
  "description": "Data reduction for Cr isotopes, calibrated for 50Cr-54Cr spike pair, with reporting of 53Cr/52Cr ratio relative to NIST SRM 3112a, on the Phoenix and Isoprobe-T TIMS at the Geology Section, Department of Geoscience and Natural Resources, University of Copenhagen",

  // The version parameter is used by the file spec_read to see if the file spec
  // is compatible with the current version of pysotope.
  "version": 2,
  // The element symbol, used for generating lookup text for ratios.
  "element" : "Cr",

  // List of column in the data files, must be formatted as:
  //   "mass_number" : column_index
  // Mass number must be enclosed in double qoutes: "49"
  // Index must be an integer: 0
  // The index starts at 0 for the first column.
  "cycle_columns" : 
    { "49" : 0, 
      "50" : 1, 
      "51" : 2, 
      "52" : 3, 
      "53" : 4, 
      "54" : 5, 
      "56" : 6 
    },
 
  // List of fractions n to report in the final data table, formatted as:
  //    ["denominator", ["numerator 1", "numerator 2", ... , "numerator n"]]
  // Mass number for denom. and numer. must be enclosed in double quotes, and
  // may not contain any text except for the mass number.
  "report_fracs" : 
    ["52", ["50", "53", "54"]],

  // Follows the same format as 'report_fracs', however may only contain
  // three numerators.
  // The denominator and first numerator should refer to the spiked isotopes,
  // And the two second numerators should be the reference isotopes.
  "reduce_fracs" : 
    ["54", ["50", "52", "53"]],
    
  // reporting of relative isotope composition, following the format:
  //   {"label 1" : ["numerator 1", "denominator", factor, include_unfiltered],
  //    "label 2" : ["numerator 2", "denominator", factor, include_unfiltered]}
  // The label may be any relevant text e.g. as shown below.
  // Numerator and denominator must be an isotope reference in double quotes e.g.
  //    "53Cr"
  // The factor is an integer multiplied to the deviation from the standard.
  //   e.g. 1000 for delta value and 10000 for epsilon value.
  // Include_unfiltered can be either true or false (case sensitive) 
  // given true statistics for non-outlier rejected data will be produced in 
  // addition to outlier-rejected statistics. false will only report outlier rejected.
  "rel_report":
    {
        "d53Cr_SRM3112a" : ["53Cr", "52Cr", 1000, true]
    },

  // Dict of used isotopes:
  //   "analyte_mass" : [["ref_mass", "interfering_element"], ...]
  // A list of used isotopes and their interferences.
  // A reference isotope must be referenced for each interfering elements.
  // An empty list [] denotes no interference correction.
  // The natural or reference ratio between the "analyte_mass" and "ref_mass"
  // of the interfering element must be denoted in "nat_ratios"
  "used_isotopes" :
    { 
      "50" : [["51", "V"], ["49", "Ti"]],
      "52" : [],
      "53" : [],
      "54" : [["56", "Fe"]]    
    },

  // A complete list of atomic masses of all isotopes used in the data reduction, 
  // incuding those of interfering elements.
  // Labels must be formatted as below with atomic number before element symbol.
  "masses" :
    { "50Cr" : 49.946049,
      "52Cr" : 51.940512,
      "53Cr" : 52.940653,
      "54Cr" : 53.938885,
      "49Ti" : 48.947871,
      "50Ti" : 49.944792,
      "51V"  : 50.943964,
      "50V"  : 49.947163,
      "54Fe" : 53.939613,
      "56Fe" : 55.934941},

  // Reference ratios for interfering elements.
  // labels must be two isotope labels, with the interfering isotope as the denominator
  // and reference isotope as numerator, these must be separated by a forward slash: /
  "nat_ratios" :
    { "49Ti/50Ti" :   1.0185185185,
      "51V/50V"   : 399.0,
      "56Fe/54Fe" :  15.698587},

  // Spike composition
  // Must contain:
  // - All isotopes of analyte element listed as mass fraction.
  // - A field labeled "amu", the atomic mass of the spike composition
  // - All ratios for the spike which can be generated by the report_fracs and reduce_fracs.
  "spike" :
    { "name" : "RF_UCPH_Cr",
      "50Cr" : 0.5379706252508730,
      "52Cr" : 0.0350570627662604,
      "53Cr" : 0.0108693041097927,
      "54Cr" : 0.4161030078730740
    },

  // Reference standard composition
  // Adheres to the same specifications as the spike compositon, but additionaly contains:
  // - An optional "name" field with a standard name, just for reference.
  // - Any ratio generated by the "rel_report" field.
  "standard" :
    { "name" : "SRM3112a",
      "50Cr" : 0.0434502788351757,
      "52Cr" : 0.8378541590693160,
      "53Cr" : 0.0950600848660935,
      "54Cr" : 0.0236354772294146
    },

  // Parameters for otlier rejection
  // - iqr_limit:    Multiple of the inter quartile range outside of which a 
  //                 point is considered an outlier
  // - max_fraction: Maximum fraction of rows rejected.
  "outlier_rejection":
    { "iqr_limit" : 1.5,
      "max_fraction" : 0.05},

  // Initial guess for inversion function
  // Mass bias factors an lambda value.
  // [alpha_nat, beta_ins, lambda]
  "initial_parameters":
    [ 0.003,-0.06,0.8 ],
  
  // Info for parsing dates reported in data files
  // See strftime.org or python 3 datetime for explanation.
  "date":{
    "field" : ["PARAMETERS", "Analysis Start Time"],
    "report_format" : "%Y-%m-%d %H:%M:%S"},
  
  // Filetype plugin
  // This is the import path to a python module able to read the specified
  // datatype. These can be installed by putting a copy of the plugin in the 
  // plugin directory under the pysotope code folder. 
  // The filetype plugin must expose a single function:
  //    read_file(file_path: str, file_spec: dict) -> dict
  // Where dict contains at a key "CYCLES" with a list of each analytical cycle
  // needed for data reduction.
  "filetype_plugin":
        "pysotope.plugins.filetype_xls",

  // Data file specification.
  // Specific for the provided xls reader, as it outputs all sheets as a single
  // csv file. Configured to read data files from the IonVantage software suite.
  "file_spec":
        {
        // This is a parameter lookup definition
        // I.e. returns a list of key value pairs
        "PARAMETERS": [ // Label in output dict
            "params", // param lookup identifier
            {
                // Search string data collection starts at the first
                // match if search_string.
                // In this case it is the name of the excel sheet.
                "start_string": "TUNING PARAMETERS", 
                // The algorightm searches for this value in the csv
                // and returns the value in the cell left of the match.
                // The params file has a colon (:) at the end of these labels
                // it is skipped in the definition.
                "labels": [ // list of lookup labels
                    "Method Name",
                    "Analysis Start Time",
                    "Cycles per Block",
                    "Number of Blocks",
                    "No. of Sequences",
                    "Sample/Vial Number",
                    "Sample ID",
                    "User name",
                    "Serial Number",
                    "XL Doc Name",
                    "Temperature (°C)",
                    "Temp Error (°C)",
                    "Current (Amps)"]
            }
        ],
        // Table lookup
        "CYCLES": [ // Label for output dict
            "table", // table lookup identifier
            { // Dictionary defining the data lookup
                // First row lookup string
                "start_string": "Cycle,Time", 
                // After last column lookup, skips any 
                // matches prior to start string
                "end_string": "\nBLOCK Data", 
                "first_col": 2, // First column to include (starts at 0)
                "n_columns": 7, // Number of columns to include
                // Number of rows to skip (value of 0 includes the row 
                // matced by the start_string)
                "skip_rows": 1 
            },
            {
                "search_string": ",Function:", // Search string to match for label row
                "first_col": 2, // Number of columns to include
                "n_columns": 7 // Number of columns to include
            }
        ],
        // Another table lookup
        "MONITORING": [
            "table",
            {
                "start_string": "FAC Temp",
                "end_string": "TUNING PARAMETERS",
                "first_col": 7,
                "n_columns": 10,
                "skip_rows": 1
            },
            {
                "search_string": "FAC Temp",
                "first_col": 7,
                "n_columns": 10
            }
        ]
    }
}