File-Format-Conversion
With the command spectrafit-file-converter input and also output files can be converted. The supported file formats are:
.json.yamlor.yml.tomlor.lock(output only)
Bash
➜ spectrafit-file-converter -h
usage: spectrafit-file-converter [-h] [-f {yml,lock,yaml,json,toml}] [-e {yml,lock,yaml,json,toml}] infile
Converter for 'SpectraFit' input and output files.
positional arguments:
infile Filename of the 'SpectraFit' input or output file.
options:
-h, --help show this help message and exit
-f {yml,lock,yaml,json,toml}, --file-format {yml,lock,yaml,json,toml}
File format for the conversion.
-e {yml,lock,yaml,json,toml}, --export-format {yml,lock,yaml,json,toml}
File format for the export.
Info
The file format change can be also applied to the .json-output to the more human-readable lock-file-format, which is a .toml file.
Both output files are provided as:
Scdoc
* example_8_summary.json
* example_8_summary.lock
JSON
{
"infile": "athena.nor",
"outfile": "example_8",
"input": "example_8.json",
"oversampling": false,
"energy_start": 5440,
"energy_stop": 5520,
"smooth": 0,
"shift": 0,
"column": [0, 1],
"separator": "\\s+",
"decimal": ".",
"header": null,
"comment": "#",
"global_": 0,
"autopeak": false,
"noplot": false,
"verbose": 0,
"description": {
"project_name": "Template",
"project_details": "Template for testing",
"keywords": [
"2D-Spectra",
"fitting",
"curve-fitting",
"peak-fitting",
"spectrum"
]
},
"minimizer": {
"nan_policy": "propagate",
"calc_covar": true
},
"optimizer": {
"max_nfev": 1000,
"method": "leastsq"
},
"report": {
"min_correl": 0.0
},
"conf_interval": null,
"peaks": {
"1": {
"pseudovoigt": {
"amplitude": {
"max": 4,
"min": 0,
"vary": true,
"value": 1
},
"center": {
"max": 5470,
"min": 5460,
"vary": true,
"value": 5468
},
"fwhmg": {
"max": 2.75,
"min": 0.001,
"vary": true,
"value": 1.0
},
"fwhml": {
"max": 2.75,
"min": 0.001,
"vary": true,
"value": 1.0
}
}
},
"2": {
"pseudovoigt": {
"amplitude": {
"max": 4,
"min": 0,
"vary": true,
"value": 1
},
"center": {
"max": 5470,
"min": 5465,
"vary": true,
"value": 5469
},
"fwhmg": {
"max": 2.75,
"min": 0.001,
"vary": true,
"value": 1.0
},
"fwhml": {
"max": 2.75,
"min": 0.001,
"vary": true,
"value": 1.0
}
}
},
"3": {
"pseudovoigt": {
"amplitude": {
"max": 4,
"min": 0,
"vary": true,
"value": 1
},
"center": {
"max": 5480,
"min": 5470,
"vary": true,
"value": 5473
},
"fwhmg": {
"max": 3.75,
"min": 0.1,
"vary": true,
"value": 1
},
"fwhml": {
"max": 3.75,
"min": 0.1,
"vary": true,
"value": 1
}
}
},
"4": {
"gaussian": {
"amplitude": {
"max": 10,
"min": 0.1,
"vary": true,
"value": 3
},
"center": {
"max": 5485,
"min": 5475,
"vary": true,
"value": 5478
},
"fwhmg": {
"max": 4,
"min": 0.1,
"vary": true,
"value": 1
}
}
},
"5": {
"gaussian": {
"amplitude": {
"max": 10,
"min": 0.1,
"vary": true,
"value": 4
},
"center": {
"max": 5498,
"min": 5480,
"vary": true,
"value": 5483
},
"fwhmg": {
"max": 4.75,
"min": 0.1,
"vary": true,
"value": 3
}
}
},
"6": {
"gaussian": {
"amplitude": {
"max": 10,
"min": 0.1,
"vary": true,
"value": 4
},
"center": {
"max": 5498,
"min": 5493,
"vary": true,
"value": 5494
},
"fwhmg": {
"max": 4.75,
"min": 0.1,
"vary": true,
"value": 3
}
}
},
"7": {
"atan": {
"amplitude": {
"max": 5,
"min": 0,
"vary": true,
"value": 1
},
"center": {
"max": 5500,
"min": 5483,
"vary": true,
"value": 5481
},
"sigma": {
"max": 0.75,
"min": 0.001,
"vary": true,
"value": 0.01
}
}
}
},
"timestamp": "2022-06-26 12:35:11",
"ID": "e5c7fc20-bd57-4578-abbf-7736cef3be9b",
"host_info": "e74490816920d147adc2315b45c4c6ce05e99ae9e09e34d2a263e2e9da861ffd",
"used_version": "0.9.0",
"data_statistic": {
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5498.20038, 5526.97246, 5602.409339999999, 5707.751
],
"1": [
393.0, 0.5559652545537828, 0.5000826290756465, -0.0015911817,
0.0011720014800000002, 0.003939243640000001, 0.012118344800000002,
0.11680503600000006, 0.55104052, 0.983449568, 1.0087658400000001,
1.04338526, 1.12497912, 1.2670019
]
},
"fit_insights": {
"configurations": {
"fitting_method": "leastsq",
"function_evals": 1000,
"data_points": 267,
"variable_names": [
"pseudovoigt_amplitude_1",
"pseudovoigt_center_1",
"pseudovoigt_fwhmg_1",
"pseudovoigt_fwhml_1",
"pseudovoigt_amplitude_2",
"pseudovoigt_center_2",
"pseudovoigt_fwhmg_2",
"pseudovoigt_fwhml_2",
"pseudovoigt_amplitude_3",
"pseudovoigt_center_3",
"pseudovoigt_fwhmg_3",
"pseudovoigt_fwhml_3",
"gaussian_amplitude_4",
"gaussian_center_4",
"gaussian_fwhmg_4",
"gaussian_amplitude_5",
"gaussian_center_5",
"gaussian_fwhmg_5",
"gaussian_amplitude_6",
"gaussian_center_6",
"gaussian_fwhmg_6",
"atan_amplitude_7",
"atan_center_7",
"atan_sigma_7"
],
"variable_numbers": 24,
"degree_of_freedom": 243
},
"statistics": {
"chi_square": 0.19287134070118112,
"reduced_chi_square": 0.0007937092209925148,
"akaike_information": -1883.2058200035844,
"bayesian_information": -1797.1118522019785
},
"variables": {
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"model_value": 6.887357351104129e-11,
"best_value": 6.887357351104129e-11
},
"pseudovoigt_center_1": {
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"model_value": 5468.054405630964,
"best_value": 5468.054405630964
},
"pseudovoigt_fwhmg_1": {
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"model_value": 0.1897199824713271,
"best_value": 0.1897199824713271
},
"pseudovoigt_fwhml_1": {
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"model_value": 1.8340047382909581,
"best_value": 1.8340047382909581
},
"pseudovoigt_amplitude_2": {
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"best_value": 1.5312014287723803
},
"pseudovoigt_center_2": {
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"model_value": 5468.965365073547,
"best_value": 5468.965365073547
},
"pseudovoigt_fwhmg_2": {
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"best_value": 2.1735730746400175
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"pseudovoigt_fwhml_2": {
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},
"pseudovoigt_amplitude_3": {
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"best_value": 1.4124892488220628
},
"pseudovoigt_center_3": {
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},
"pseudovoigt_fwhmg_3": {
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},
"pseudovoigt_fwhml_3": {
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"best_value": 3.7499977334701127
},
"gaussian_amplitude_4": {
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"best_value": 0.6090009741875487
},
"gaussian_center_4": {
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"best_value": 5477.92439530641
},
"gaussian_fwhmg_4": {
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"best_value": 2.5805286730950385
},
"gaussian_amplitude_5": {
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"best_value": 3.2112928728775594
},
"gaussian_center_5": {
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"best_value": 5481.724992617458
},
"gaussian_fwhmg_5": {
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"best_value": 4.1240411794396445
},
"gaussian_amplitude_6": {
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"best_value": 1.2428818045605532
},
"gaussian_center_6": {
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"model_value": 5493.950495823278,
"best_value": 5493.950495823278
},
"gaussian_fwhmg_6": {
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"best_value": 4.749999999999982
},
"atan_amplitude_7": {
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"best_value": 1.0784237600535795
},
"atan_center_7": {
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"model_value": 5483.0,
"best_value": 5483.0
},
"atan_sigma_7": {
"init_value": 0.01,
"model_value": 0.7490707110057951,
"best_value": 0.7490707110057951
}
},
"errorbars": {
"at_boundary": "atan_center_7",
"at_initial_value": "atan_center_7"
},
"correlations": {
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"pseudovoigt_center_1": {},
"pseudovoigt_fwhmg_1": {},
"pseudovoigt_fwhml_1": {},
"pseudovoigt_amplitude_2": {},
"pseudovoigt_center_2": {},
"pseudovoigt_fwhmg_2": {},
"pseudovoigt_fwhml_2": {},
"pseudovoigt_amplitude_3": {},
"pseudovoigt_center_3": {},
"pseudovoigt_fwhmg_3": {},
"pseudovoigt_fwhml_3": {},
"gaussian_amplitude_4": {},
"gaussian_center_4": {},
"gaussian_fwhmg_4": {},
"gaussian_amplitude_5": {},
"gaussian_center_5": {},
"gaussian_fwhmg_5": {},
"gaussian_amplitude_6": {},
"gaussian_center_6": {},
"gaussian_fwhmg_6": {},
"atan_amplitude_7": {},
"atan_center_7": {},
"atan_sigma_7": {}
},
"covariance_matrix": {}
},
"linear_correlation": {
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"residual": [
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}
TOML
infile = "athena.nor"
outfile = "example_8"
input = "example_8.json"
oversampling = false
energy_start = 5440
energy_stop = 5520
smooth = 0
shift = 0
column = [0, 1]
separator = "\\s+"
decimal = "."
comment = "#"
global_ = 0
autopeak = false
noplot = false
version = false
verbose = 0
timestamp = "2022-06-26 12:35:11"
ID = "e5c7fc20-bd57-4578-abbf-7736cef3be9b"
host_info = "e74490816920d147adc2315b45c4c6ce05e99ae9e09e34d2a263e2e9da861ffd"
host_info = "e74490816920d147adc2315b45c4c6ce05e99ae9e09e34d2a263e2e9da861ffd"
used_version = "0.9.0"
[description]
project_name = "Template"
project_details = "Template for testing"
keywords = [
"2D-Spectra",
"fitting",
"curve-fitting",
"peak-fitting",
"spectrum",
]
[minimizer]
nan_policy = "propagate"
calc_covar = true
[optimizer]
max_nfev = 1000
method = "leastsq"
[report]
min_correl = 0.0
[data_statistic]
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[linear_correlation]
energy = [
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[fit_result]
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[fit_insights.configurations]
fitting_method = "leastsq"
function_evals = 1000
data_points = 267
variable_names = [
"pseudovoigt_amplitude_1",
"pseudovoigt_center_1",
"pseudovoigt_fwhmg_1",
"pseudovoigt_fwhml_1",
"pseudovoigt_amplitude_2",
"pseudovoigt_center_2",
"pseudovoigt_fwhmg_2",
"pseudovoigt_fwhml_2",
"pseudovoigt_amplitude_3",
"pseudovoigt_center_3",
"pseudovoigt_fwhmg_3",
"pseudovoigt_fwhml_3",
"gaussian_amplitude_4",
"gaussian_center_4",
"gaussian_fwhmg_4",
"gaussian_amplitude_5",
"gaussian_center_5",
"gaussian_fwhmg_5",
"gaussian_amplitude_6",
"gaussian_center_6",
"gaussian_fwhmg_6",
"atan_amplitude_7",
"atan_center_7",
"atan_sigma_7",
]
variable_numbers = 24
degree_of_freedom = 243
[fit_insights.statistics]
chi_square = 0.19287134070118112
reduced_chi_square = 0.0007937092209925148
akaike_information = -1883.2058200035844
bayesian_information = -1797.1118522019785
[fit_insights.errorbars]
at_boundary = "atan_center_7"
at_initial_value = "atan_center_7"
[fit_insights.covariance_matrix]
[fit_insights.variables.pseudovoigt_amplitude_1]
init_value = 1
model_value = 6.887357351104129e-11
best_value = 6.887357351104129e-11
[fit_insights.variables.pseudovoigt_center_1]
init_value = 5468
model_value = 5468.054405630964
best_value = 5468.054405630964
[fit_insights.variables.pseudovoigt_fwhmg_1]
init_value = 1.0
model_value = 0.1897199824713271
best_value = 0.1897199824713271
[fit_insights.variables.pseudovoigt_fwhml_1]
init_value = 1.0
model_value = 1.8340047382909581
best_value = 1.8340047382909581
[fit_insights.variables.pseudovoigt_amplitude_2]
init_value = 1
model_value = 1.5312014287723803
best_value = 1.5312014287723803
[fit_insights.variables.pseudovoigt_center_2]
init_value = 5469
model_value = 5468.965365073547
best_value = 5468.965365073547
[fit_insights.variables.pseudovoigt_fwhmg_2]
init_value = 1.0
model_value = 2.1735730746400175
best_value = 2.1735730746400175
[fit_insights.variables.pseudovoigt_fwhml_2]
init_value = 1.0
model_value = 1.429425183820899
best_value = 1.429425183820899
[fit_insights.variables.pseudovoigt_amplitude_3]
init_value = 1
model_value = 1.4124892488220628
best_value = 1.4124892488220628
[fit_insights.variables.pseudovoigt_center_3]
init_value = 5473
model_value = 5475.767047063245
best_value = 5475.767047063245
[fit_insights.variables.pseudovoigt_fwhmg_3]
init_value = 1
model_value = 0.10000000837664919
best_value = 0.10000000837664919
[fit_insights.variables.pseudovoigt_fwhml_3]
init_value = 1
model_value = 3.7499977334701127
best_value = 3.7499977334701127
[fit_insights.variables.gaussian_amplitude_4]
init_value = 3
model_value = 0.6090009741875487
best_value = 0.6090009741875487
[fit_insights.variables.gaussian_center_4]
init_value = 5478
model_value = 5477.92439530641
best_value = 5477.92439530641
[fit_insights.variables.gaussian_fwhmg_4]
init_value = 1
model_value = 2.5805286730950385
best_value = 2.5805286730950385
[fit_insights.variables.gaussian_amplitude_5]
init_value = 4
model_value = 3.2112928728775594
best_value = 3.2112928728775594
[fit_insights.variables.gaussian_center_5]
init_value = 5483
model_value = 5481.724992617458
best_value = 5481.724992617458
[fit_insights.variables.gaussian_fwhmg_5]
init_value = 3
model_value = 4.1240411794396445
best_value = 4.1240411794396445
[fit_insights.variables.gaussian_amplitude_6]
init_value = 4
model_value = 1.2428818045605532
best_value = 1.2428818045605532
[fit_insights.variables.gaussian_center_6]
init_value = 5494
model_value = 5493.950495823278
best_value = 5493.950495823278
[fit_insights.variables.gaussian_fwhmg_6]
init_value = 3
model_value = 4.749999999999982
best_value = 4.749999999999982
[fit_insights.variables.atan_amplitude_7]
init_value = 1
model_value = 1.0784237600535795
best_value = 1.0784237600535795
[fit_insights.variables.atan_center_7]
init_value = 5483
model_value = 5483.0
best_value = 5483.0
[fit_insights.variables.atan_sigma_7]
init_value = 0.01
model_value = 0.7490707110057951
best_value = 0.7490707110057951
[fit_insights.correlations.pseudovoigt_amplitude_1]
[fit_insights.correlations.pseudovoigt_center_1]
[fit_insights.correlations.pseudovoigt_fwhmg_1]
[fit_insights.correlations.pseudovoigt_fwhml_1]
[fit_insights.correlations.pseudovoigt_amplitude_2]
[fit_insights.correlations.pseudovoigt_center_2]
[fit_insights.correlations.pseudovoigt_fwhmg_2]
[fit_insights.correlations.pseudovoigt_fwhml_2]
[fit_insights.correlations.pseudovoigt_amplitude_3]
[fit_insights.correlations.pseudovoigt_center_3]
[fit_insights.correlations.pseudovoigt_fwhmg_3]
[fit_insights.correlations.pseudovoigt_fwhml_3]
[fit_insights.correlations.gaussian_amplitude_4]
[fit_insights.correlations.gaussian_center_4]
[fit_insights.correlations.gaussian_fwhmg_4]
[fit_insights.correlations.gaussian_amplitude_5]
[fit_insights.correlations.gaussian_center_5]
[fit_insights.correlations.gaussian_fwhmg_5]
[fit_insights.correlations.gaussian_amplitude_6]
[fit_insights.correlations.gaussian_center_6]
[fit_insights.correlations.gaussian_fwhmg_6]
[fit_insights.correlations.atan_amplitude_7]
[fit_insights.correlations.atan_center_7]
[fit_insights.correlations.atan_sigma_7]
[peaks.1.pseudovoigt.amplitude]
max = 4
min = 0
vary = true
value = 1
[peaks.1.pseudovoigt.center]
max = 5470
min = 5460
vary = true
value = 5468
[peaks.1.pseudovoigt.fwhmg]
max = 2.75
min = 0.001
vary = true
value = 1.0
[peaks.1.pseudovoigt.fwhml]
max = 2.75
min = 0.001
vary = true
value = 1.0
[peaks.2.pseudovoigt.amplitude]
max = 4
min = 0
vary = true
value = 1
[peaks.2.pseudovoigt.center]
max = 5470
min = 5465
vary = true
value = 5469
[peaks.2.pseudovoigt.fwhmg]
max = 2.75
min = 0.001
vary = true
value = 1.0
[peaks.2.pseudovoigt.fwhml]
max = 2.75
min = 0.001
vary = true
value = 1.0
[peaks.3.pseudovoigt.amplitude]
max = 4
min = 0
vary = true
value = 1
[peaks.3.pseudovoigt.center]
max = 5480
min = 5470
vary = true
value = 5473
[peaks.3.pseudovoigt.fwhmg]
max = 3.75
min = 0.1
vary = true
value = 1
[peaks.3.pseudovoigt.fwhml]
max = 3.75
min = 0.1
vary = true
value = 1
[peaks.4.gaussian.amplitude]
max = 10
min = 0.1
vary = true
value = 3
[peaks.4.gaussian.center]
max = 5485
min = 5475
vary = true
value = 5478
[peaks.4.gaussian.fwhmg]
max = 4
min = 0.1
vary = true
value = 1
[peaks.5.gaussian.amplitude]
max = 10
min = 0.1
vary = true
value = 4
[peaks.5.gaussian.center]
max = 5498
min = 5480
vary = true
value = 5483
[peaks.5.gaussian.fwhmg]
max = 4.75
min = 0.1
vary = true
value = 3
[peaks.6.gaussian.amplitude]
max = 10
min = 0.1
vary = true
value = 4
[peaks.6.gaussian.center]
max = 5498
min = 5493
vary = true
value = 5494
[peaks.6.gaussian.fwhmg]
max = 4.75
min = 0.1
vary = true
value = 3
[peaks.7.atan.amplitude]
max = 5
min = 0
vary = true
value = 1
[peaks.7.atan.center]
max = 5500
min = 5483
vary = true
value = 5481
[peaks.7.atan.sigma]
max = 0.75
min = 0.001
vary = true
value = 0.01