Multi Peak Fitting

In this example, the the input-file of SpectraFit is used to perform a multi peak fitting, shown in the figure below.

Mulit peak fitting example by using 6 different pseudovoigt functions. The energy range is limited from -1 to 2.4 eV.

All required settings are defined in the input-file in the section settings.

settings

If the data source, named infile is defined in the input-file, any filename can be used, like the undersocore _.

Bash

spectrafit _ -i example_2.json

In this particular example, some of the pre-defined peaks are fixed. This is also printed in the terminal output:

Bash

[[Variables]]
    pseudovoigt_amplitude_1:  0.31188533 (init = 1), model_value = 0.3118853
    pseudovoigt_center_1:     0.01664784 (init = 0), model_value = 0.01664784
    pseudovoigt_fwhmg_1:     0.14329487 (init = 0.01), model_value = 0.1432949
    pseudovoigt_fwhml_1:     0.19995302 (init = 0.01), model_value = 0.199953
    pseudovoigt_amplitude_2:  0.01669370 (init = 1), model_value = 0.0166937
    pseudovoigt_center_2:     1.662 (fixed)
    pseudovoigt_fwhmg_2:     0.28628541 (init = 0.02), model_value = 0.2862854
    pseudovoigt_fwhml_2:     0.12531854 (init = 0.01), model_value = 0.1253185
    pseudovoigt_amplitude_3:  0.02456846 (init = 1), model_value = 0.02456846
    pseudovoigt_center_3:     1.924 (fixed)
    pseudovoigt_fwhmg_3:     0.43336697 (init = 0.01), model_value = 0.433367
    pseudovoigt_fwhml_3:     0.10962934 (init = 0.01), model_value = 0.1096293
    pseudovoigt_amplitude_4:  4.1999e-05 (init = 1), model_value = 4.199897e-05
    pseudovoigt_center_4:     2 (fixed)
    pseudovoigt_fwhmg_4:     0.01376736 (init = 0.01), model_value = 0.01376736
    pseudovoigt_fwhml_4:     0.08425184 (init = 0.01), model_value = 0.08425184
    pseudovoigt_amplitude_5:  0.14042084 (init = 1), model_value = 0.1404208
    pseudovoigt_center_5:     2.345 (fixed)
    pseudovoigt_fwhmg_5:     0.20598429 (init = 0.01), model_value = 0.2059843
    pseudovoigt_fwhml_5:     0.53558371 (init = 0.01), model_value = 0.5355837

example_2.json

JSON

{
"settings": {
    "column": [0, 1],
    "decimal": ".",
    "energy_start": -1,
    "energy_stop": 2.4,
    "header": null,
    "infile": "data.txt",
    "outfile": "example_2_results",
    "oversampling": false,
    "separator": "\t",
    "shift": 0,
    "smooth": 0,
    "verbose": 1
},
"fitting": {
    "description": {
    "project_name": "Template",
    "project_details": "Template for testing",
    "keywords": [
        "2D-Spectra",
        "fitting",
        "curve-fitting",
        "peak-fitting",
        "spectrum"
    ]
    },

    "parameters": {
    "minimizer": { "nan_policy": "propagate", "calc_covar": true },
    "optimizer": { "max_nfev": 1000, "method": "leastsq" },
    "report": { "min_correl": 0.0 }
    },
    "peaks": {
    "1": {
        "pseudovoigt": {
        "amplitude": {
            "max": 2,
            "min": 0,
            "vary": true,
            "value": 1
        },
        "center": {
            "max": 0.5,
            "min": -0.5,
            "vary": true,
            "value": 0
        },
        "fwhmg": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        },
        "fwhml": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        }
        }
    },
    "2": {
        "pseudovoigt": {
        "amplitude": {
            "max": 2,
            "min": 0,
            "vary": true,
            "value": 1
        },
        "center": {
            "max": 2,
            "min": 0,
            "vary": false,
            "value": 1.662
        },
        "fwhmg": {
            "max": 0.5,
            "min": 0.02,
            "vary": true,
            "value": 0.01
        },
        "fwhml": {
            "max": 0.5,
            "min": 0.01,
            "vary": true,
            "value": 0.01
        }
        }
    },
    "3": {
        "pseudovoigt": {
        "amplitude": {
            "max": 2,
            "min": 0,
            "vary": true,
            "value": 1
        },
        "center": {
            "max": 2,
            "min": 1.8,
            "vary": false,
            "value": 1.924
        },
        "fwhmg": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        },
        "fwhml": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        }
        }
    },
    "4": {
        "pseudovoigt": {
        "amplitude": {
            "max": 2,
            "min": 0,
            "vary": true,
            "value": 1
        },
        "center": {
            "max": 2,
            "min": 1,
            "vary": false,
            "value": 2.157
        },
        "fwhmg": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        },
        "fwhml": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        }
        }
    },
    "5": {
        "pseudovoigt": {
        "amplitude": {
            "max": 2,
            "min": 0,
            "vary": true,
            "value": 1
        },
        "center": {
            "max": 2.5,
            "min": 2,
            "vary": false,
            "value": 2.345
        },
        "fwhmg": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        },
        "fwhml": {
            "max": 0.75,
            "min": 0.001,
            "vary": true,
            "value": 0.01
        }
        }
    }
    }
}
}