Normalizing and Transforming Data

Before performing model calculations on your data, it may be desired to normalize the input composition to a total of 100 wt%. VESIcal has multiple methods for normalizing sample data using various routines. Each of the normalization routines can be accessed by the user at any time to normalize either a signle sample or all samples in a BatchFile object.

The standard normalization type returns the composition normalized to 100%, including any volatiles. The FixedVolatiles type the oxides to 100%, but volatiles remain fixed while other major element oxides are reduced proporitonally so that the total is 100 wt%. The AdditionalVolatiles type normalizes oxides to 100% assuming the sample is volatile-free. If H2O or CO2 concentrations are passed to the function, their un-normalized values will be retained in addition to the normalized non-volatile oxides, summing to >100%.

Normalization types are: ‘none’, ‘standard’, ‘fixedvolatiles’, ‘additionalvolatiles’.

import VESIcal as v

Default normalizations and how to change them

MagmaSat

Currently, no models force any kind of normalization onto samples. For testing purposes, MagmaSat (the default model) has an attribute called ‘normalization_type’. By default, this is set to ‘none’ such that no normalization is performed on samples. To change the type of normalization performed during all calculations, you can create a copy of the MagmaSat() model object, set its normalization type, and then use that model object for calculations, like so:

# make a copy of the MagmaSat() model object and give it a name
magmasatNorm = v.models.magmasat.MagmaSat()

# set normalization_type to be whatever you want. Let's say 'standard'.
magmasatNorm.normalization_type = 'standard'

# now you can do a calculation and set model=magmasatNorm
test_calc = v.calculate_saturation_pressure(sample=<your-sample>, temperature=<temperature>, model=magmasatNorm).result

Normalizing an entire dataset

Import an Excel file

myfile = v.BatchFile('example_data.xlsx')
myfile.get_data()
Output
Label SiO2 TiO2 Al2O3 Fe2O3 Cr2O3 FeO MnO MgO NiO CoO CaO Na2O K2O P2O5 H2O CO2 Press Temp
BT-ex 77.5 0.08 12.5 0.207 0 0.473 0 0.03 0 0 0.43 3.98 4.88 0 5.5 0.05 500 900
TVZMa-ex 78.37 0.13 11.94 0 0 0.99 0.04 0.05 0 0 0.53 3.8 4.14 0 4.06 0.005 600 800
TVZOh-ex 77.9 0.08 12.15 0 0 0.95 0.05 0.06 0 0 0.55 4.05 4.12 0 4.63 0.005 50 900
Oh48-FTIR1-MI1-a 78.27 0.0298 12.02 0 0 0.9828 0.0336 0.0515 0 0 0.4772 4.05 4.09 0 4.214912406 0.004565932 250 950
Oh48-FTIR1-MI1-b 78.27 0.0298 12.02 0 0 0.9828 0.0336 0.0515 0 0 0.4772 4.05 4.09 0 4.005815793 0.004447963 500 1025
Oh48-FTIR1-MI1-IRc 78.27 0.0298 12.02 0 0 0.9828 0.0336 0.0515 0 0 0.4772 4.05 4.09 0 3.885649341 0.004654367 5000 925
Oh50-4.1 77.91 0.0984 12.07 0 0 1.0556 0.0257 0.0999 0 0 0.5216 4.04 4.18 0 4.641842879 0.004565932 1000 862
Oh50-4.2 77.91 0.0984 12.07 0 0 1.0556 0.0257 0.0999 0 0 0.5216 4.04 4.18 0 4.402133476 0.004447963 100 770
Oh49-4.1 77.92 0.0099 12.11 0 0 1.002 0.0672 0.0546 0 0 0.5346 4.01 4.3 0 4.283934433 0.004565932 1000 855
Oh49-4.2 77.92 0.0099 12.11 0 0 1.002 0.0672 0.0546 0 0 0.5346 4.01 4.3 0 4.230532593 0.004447963 500 1000
Ma55-5a.1 77.68 0.0096 12.27 0 0 1.0272 0.0628 0.0342 0 0 0.6064 3.97 4.35 0 4.459767403 0.004654367 5000 1010
Ma57-3b.2 77.9 0.0498 12.07 0 0 1.0844 0.0748 0.0355 0 0 0.4759 4.1 4.21 0 3.712506046 0.004447963 1000 1012
Ma57-3c.1 77.65 0.159 12.28 0 0 0.9769 0.0597 0.0577 0 0 0.5598 4.08 4.18 0.0064 4.443973024 0.004654367 100 885
Ma57-3c.2 77.65 0.159 12.28 0 0 0.9769 0.0597 0.0577 0 0 0.5598 4.08 4.18 0.0064 4.283171078 0.004644523 1000 885

Standard Normalization

Returns the composition normalized to 100%, including any volatiles.

standard = myfile.get_data(normalization='standard', asBatchFile=True)
standard.get_data()
Output
Label SiO2 TiO2 Al2O3 Fe2O3 Cr2O3 FeO MnO MgO NiO CoO CaO Na2O K2O P2O5 H2O CO2 Press Temp
BT-ex 73.36930796 0.07573606 11.83375935 0.195967055 0 0.447789454 0 0.028401022 0 0 0.407081322 3.767868977 4.61989965 0 5.206854113 0.047335037 500 900
TVZMa-ex 75.31593869 0.124933929 11.47470088 0 0 0.951419922 0.038441209 0.048051511 0 0 0.509346019 3.651914853 3.978665129 0 3.901782711 0.004805151 600 800
TVZOh-ex 74.51336745 0.076522072 11.62178966 0 0 0.908699603 0.047826295 0.057391554 0 0 0.526089244 3.873929887 3.9408867 0 4.428714907 0.004782629 50 900
Oh48-FTIR1-MI1-a 75.09759353 0.028592159 11.53281045 0 0 0.942965567 0.032238139 0.049412624 0 0 0.457858332 3.885847116 3.924225853 0 4.044075363 0.004380868 250 950
Oh48-FTIR1-MI1-b 75.24864373 0.028649669 11.55600738 0 0 0.944862234 0.032302982 0.049512012 0 0 0.458779261 3.893663052 3.932118984 0 3.851184431 0.004276264 500 1025
Oh48-FTIR1-MI1-IRc 75.33552773 0.028682749 11.56935024 0 0 0.945953196 0.03234028 0.049569179 0 0 0.45930898 3.898158775 3.936659108 0 3.739969895 0.004479867 5000 925
Oh50-4.1 74.44986167 0.09402986 11.53394725 0 0 1.008718701 0.024558612 0.095463242 0 0 0.498434705 3.860575551 3.994357872 0 4.435689389 0.00436315 1000 862
Oh50-4.2 74.62087493 0.094245849 11.56044103 0 0 1.011035754 0.024615024 0.095682523 0 0 0.499579622 3.869443392 4.003533015 0 4.216288686 0.004260184 100 770
Oh49-4.1 74.7098662 0.009492142 11.61109445 0 0 0.960719789 0.064431507 0.052350599 0 0 0.512575648 3.844796759 4.122849392 0 4.107445692 0.004377826 1000 855
Oh49-4.2 74.74822318 0.009497015 11.61705573 0 0 0.961213034 0.064464587 0.052377477 0 0 0.51283881 3.846770726 4.124966115 0 4.058326418 0.004266907 500 1000
Ma55-5a.1 74.35298514 0.009188834 11.74447899 0 0 0.983205282 0.060110292 0.032735223 0 0 0.580428041 3.799965899 4.163690594 0 4.268756687 0.004455022 5000 1010
Ma57-3b.2 75.10797083 0.048015108 11.63739676 0 0 1.045533807 0.072119079 0.034227638 0 0 0.458843175 3.953051097 4.059108565 0 3.579445389 0.004288543 1000 1012
Ma57-3c.1 74.33600615 0.152214101 11.7559067 0 0 0.935207269 0.057152087 0.055237444 0 0 0.535908516 3.905871282 4.001603422 0.006126857 4.254310445 0.004455725 100 885
Ma57-3c.2 74.45062181 0.152448794 11.77403266 0 0 0.936649227 0.057240208 0.055322613 0 0 0.536734811 3.911893587 4.007773331 0.006136304 4.106693498 0.004453156 1000 885

FixedVolatiles Normalization

Normalizes the oxides to 100%, but volatiles remain fixed while other major element oxides are reduced proporitonally so that the total is 100 wt%.

fixed_vols = myfile.get_data(normalization='fixedvolatiles', asBatchFile=True)
fixed_vols.get_data()
Output
Label SiO2 TiO2 Al2O3 Fe2O3 Cr2O3 FeO MnO MgO NiO CoO CaO Na2O K2O P2O5 H2O CO2 Press Temp
BT-ex 73.14023781 0.0754996 11.79681255 0.195355216 0 0.446391387 0 0.02831235 0 0 0.405810352 3.756105116 4.60547562 0 5.5 0.05 500 900
TVZMa-ex 75.19177868 0.124727973 11.45578458 0 0 0.949851485 0.038377838 0.047972297 0 0 0.508506351 3.645894589 3.972106211 0 4.06 0.005 600 800
TVZOh-ex 74.35625563 0.076360725 11.59728506 0 0 0.906783605 0.047725453 0.057270543 0 0 0.524979982 3.865761686 3.93257732 0 4.63 0.005 50 900
Oh48-FTIR1-MI1-a 74.96374108 0.028541197 11.5122546 0 0 0.941284844 0.032180678 0.049324552 0 0 0.457042254 3.87892106 3.917231392 0 4.214912406 0.004565932 250 950
Oh48-FTIR1-MI1-b 75.12748531 0.02860354 11.53740096 0 0 0.943340904 0.032250971 0.049432292 0 0 0.458040577 3.887393836 3.925787849 0 4.005815793 0.004447963 500 1025
Oh48-FTIR1-MI1-IRc 75.22137344 0.028639286 11.55181946 0 0 0.944519814 0.032291276 0.049494068 0 0 0.458612999 3.892251979 3.930693974 0 3.885649341 0.004654367 5000 925
Oh50-4.1 74.28909143 0.093826808 11.50904035 0 0 1.00654043 0.024505579 0.095257095 0 0 0.497358363 3.852238857 3.985732283 0 4.641842879 0.004565932 1000 862
Oh50-4.2 74.47593869 0.094062795 11.53798716 0 0 1.009072017 0.024567214 0.095496679 0 0 0.498609288 3.861927767 3.995756947 0 4.402133476 0.004447963 100 770
Oh49-4.1 74.57221102 0.009474652 11.58970066 0 0 0.958949634 0.06431279 0.052254142 0 0 0.511631212 3.837712605 4.115252918 0 4.283934433 0.004565932 1000 855
Oh49-4.2 74.6139102 0.00947995 11.59618137 0 0 0.959485857 0.064348752 0.052283361 0 0 0.511917305 3.839858571 4.117554079 0 4.230532593 0.004447963 500 1000
Ma55-5a.1 74.20446831 0.00917048 11.7210199 0 0 0.981241373 0.059990224 0.032669835 0 0 0.579268661 3.792375633 4.155373805 0 4.459767403 0.004654367 5000 1010
Ma57-3b.2 75.00419281 0.047948765 11.62131717 0 0 1.044089174 0.07201943 0.034180345 0 0 0.458209183 3.947589095 4.053500022 0 3.712506046 0.004447963 1000 1012
Ma57-3c.1 74.18859291 0.151912251 11.73259396 0 0 0.933352691 0.057038751 0.055127905 0 0 0.534845774 3.89812568 3.993667977 0.006114707 4.443973024 0.004654367 100 885
Ma57-3c.2 74.31345141 0.152167917 11.75233977 0 0 0.934923512 0.057134746 0.055220684 0 0 0.535745912 3.904686178 4.000389271 0.006124998 4.283171078 0.004644523 1000 885

AdditionalVolatiles Normalization

Normalizes oxides to 100% assuming the sample is volatile-free. If H_2O or CO_2 concentrations are passed to the function, their un-normalized values will be retained in addition to the normalized non-volatile oxides, summing to >100%.

additional_vols = myfile.get_data(normalization='additionalvolatiles', asBatchFile=True)
additional_vols.get_data()
Output
Label SiO2 TiO2 Al2O3 Fe2O3 Cr2O3 FeO MnO MgO NiO CoO CaO Na2O K2O P2O5 H2O CO2 Press Temp
BT-ex 77.43804956 0.079936051 12.49000799 0.206834532 0 0.472621902 0 0.029976019 0 0 0.429656275 3.976818545 4.876099121 0 5.5 0.05 500 900
TVZMa-ex 78.37783778 0.130013001 11.94119412 0 0 0.99009901 0.040004 0.050005001 0 0 0.530053005 3.800380038 4.140414041 0 4.06 0.005 600 800
TVZOh-ex 77.97017316 0.080072065 12.16094485 0 0 0.95085577 0.050045041 0.060054049 0 0 0.550495446 4.053648283 4.12371134 0 4.63 0.005 50 900
Oh48-FTIR1-MI1-a 78.26616496 0.02979854 12.01941105 0 0 0.982751845 0.033598354 0.051497477 0 0 0.477176618 4.04980156 4.0897996 0 4.214912406 0.004565932 250 950
Oh48-FTIR1-MI1-b 78.26616496 0.02979854 12.01941105 0 0 0.982751845 0.033598354 0.051497477 0 0 0.477176618 4.04980156 4.0897996 0 4.005815793 0.004447963 500 1025
Oh48-FTIR1-MI1-IRc 78.26616496 0.02979854 12.01941105 0 0 0.982751845 0.033598354 0.051497477 0 0 0.477176618 4.04980156 4.0897996 0 3.885649341 0.004654367 5000 925
Oh50-4.1 77.90906509 0.098398819 12.06985516 0 0 1.055587333 0.025699692 0.099898801 0 0 0.521593741 4.039951521 4.179949841 0 4.641842879 0.004565932 1000 862
Oh50-4.2 77.90906509 0.098398819 12.06985516 0 0 1.055587333 0.025699692 0.099898801 0 0 0.521593741 4.039951521 4.179949841 0 4.402133476 0.004447963 100 770
Oh49-4.1 77.91353318 0.009899178 12.10899495 0 0 1.001916841 0.067194423 0.054595469 0 0 0.534555632 4.009667198 4.29964313 0 4.283934433 0.004565932 1000 855
Oh49-4.2 77.91353318 0.009899178 12.10899495 0 0 1.001916841 0.067194423 0.054595469 0 0 0.534555632 4.009667198 4.29964313 0 4.230532593 0.004447963 500 1000
Ma55-5a.1 77.67207745 0.009599021 12.26874859 0 0 1.027095236 0.062793595 0.034196512 0 0 0.606338154 3.969595101 4.349556345 0 4.459767403 0.004654367 5000 1010
Ma57-3b.2 77.8996884 0.049799801 12.06995172 0 0 1.084395662 0.074799701 0.035499858 0 0 0.475898096 4.0999836 4.20998316 0 3.712506046 0.004447963 1000 1012
Ma57-3c.1 77.64262395 0.158984896 12.27883351 0 0 0.976807203 0.059694329 0.057694519 0 0 0.559746824 4.079612437 4.179602938 0.006399392 4.443973024 0.004654367 100 885
Ma57-3c.2 77.64262395 0.158984896 12.27883351 0 0 0.976807203 0.059694329 0.057694519 0 0 0.559746824 4.079612437 4.179602938 0.006399392 4.283171078 0.004644523 1000 885

Normalize a single sample composition

Extract a single sample from your dataset

Here, a composition is extracted from a BatchFile object and returned as a Sample object. Set asSampleClass=False to return as a dictionary.

SampleName = 'BT-ex'
extracted_bulk_comp = myfile.get_sample_composition(SampleName, asSampleClass=True)

The normalization type can be passed to get_sample_composition directly:

extracted_bulk_comp = myfile.get_sample_composition(SampleName, normalization=<normalization-type>, asSampleClass=True)

Or, normalization can be done to any Sample object, as shown below.

Standard Normalization

In the following three examples, the normalized composition is returned as a dictionary, not as a Sample object.

single_standard = extracted_bulk_comp.get_composition(normalization='standard')
single_standard

{'SiO2': 73.3693079617533,
 'TiO2': 0.07573605983148728,
 'Al2O3': 11.833759348669886,
 'Fe2O3': 0.1959670548139733,
 'Cr2O3': 0.0,
 'FeO': 0.44778945375366846,
 'MnO': 0.0,
 'MgO': 0.028401022436807727,
 'NiO': 0.0,
 'CoO': 0.0,
 'CaO': 0.4070813215942441,
 'Na2O': 3.7678689766164917,
 'K2O': 4.619899649720724,
 'P2O5': 0.0,
 'H2O': 5.2068541134147495,
 'CO2': 0.04733503739467954}

FixedVolatiles Normalization

single_fixed = extracted_bulk_comp.get_composition(normalization='fixedvolatiles')
single_fixed

{'SiO2': 73.1402378097522,
 'TiO2': 0.07549960031974419,
 'Al2O3': 11.79681254996003,
 'Fe2O3': 0.19535521582733809,
 'Cr2O3': 0.0,
 'FeO': 0.4463913868904875,
 'MnO': 0.0,
 'MgO': 0.02831235011990407,
 'NiO': 0.0,
 'CoO': 0.0,
 'CaO': 0.405810351718625,
 'Na2O': 3.756105115907274,
 'K2O': 4.6054756195043955,
 'P2O5': 0.0,
 'CO2': 0.05,
 'H2O': 5.5}

AdditionalVolatiles Normalization

single_additional = extracted_bulk_comp.get_composition(normalization='additionalvolatiles')
single_additional

{'SiO2': 77.4380495603517,
 'TiO2': 0.07993605115907274,
 'Al2O3': 12.490007993605113,
 'Fe2O3': 0.20683453237410068,
 'Cr2O3': 0.0,
 'FeO': 0.4726219024780175,
 'MnO': 0.0,
 'MgO': 0.029976019184652272,
 'NiO': 0.0,
 'CoO': 0.0,
 'CaO': 0.4296562749800159,
 'Na2O': 3.9768185451638685,
 'K2O': 4.8760991207034365,
 'P2O5': 0.0,
 'H2O': 5.5,
 'CO2': 0.05}