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Importing Excel files

This notebook shows how to import data which is stored in excel. This may be an old supplement of someones MELTS models, it may be a spreadsheet of melt inclusion or glass compositions etc
You can download the files here:
https://github.com/PennyWieser/PySulfSat/blob/main/docs/Examples/Data_Input/Dataset_S1.xlsx
https://github.com/PennyWieser/PySulfSat/blob/main/docs/Examples/Data_Input/Glass_input_example.xlsx

If you havent done so already, you need to pip install PySulfSat

Do this by removing the #. You only need to do this once per computer. After your initial installation, you will want to upgrade instead using the second command

[1]:

#!pip install PySulfSat
#!pip install PySulfSat --upgrade

[2]:

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import PySulfSat as ss
pd.options.display.max_columns = None
ss.__version__

[2]:

'0.0.17'

Importing a spreadsheet

Here we import MELTS models which have already been reformatted (e.g. in supporting information)

[3]:

df_out=ss.import_data('Dataset_S1.xlsx', sheet_name='MELTS_Model_01H2O', suffix="_Liq")
df_out.head()

We have replaced all missing liquid oxides and strings with zeros.

[3]:

	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	H2O_Liq	Temp (K) MELTS_Liq	FeO_Liq	Fe2O3_Liq	H2O_Incom_Liq	Temp_HT1987_C_Liq	Factor_Liq	H2O_test_Liq	Sample_ID_Liq_Liq
0	51.456179	2.601690	13.529073	11.114610	0.185873	6.698477	10.974609	2.406926	0.483801	0.248535	0.101655	1445.220313	9.447747	1.852481	0.514405	1148.639387	1.000000	0.514405	0
1	51.458756	2.620771	13.619359	11.144152	0.187638	6.602326	10.898161	2.428038	0.488395	0.250895	0.102621	1443.220313	9.475545	1.854419	0.519548	1146.706750	1.009998	0.519548	1
2	51.462403	2.641448	13.717522	11.175642	0.189570	6.497934	10.814571	2.451116	0.493423	0.253478	0.103677	1441.220313	9.505299	1.856348	0.524889	1144.608472	1.020381	0.524889	2
3	51.469782	2.672548	13.761157	11.246506	0.192293	6.408435	10.713787	2.472653	0.500306	0.257120	0.105167	1439.220313	9.568634	1.864716	0.535182	1142.809538	1.040389	0.535182	3
4	51.481354	2.721741	13.714324	11.384440	0.196378	6.342291	10.585430	2.491197	0.510364	0.262582	0.107401	1437.220313	9.688901	1.884351	0.546507	1141.480047	1.062405	0.546507	4

[4]:

Smythe_CalcSulf=ss.calculate_S2017_SCSS(df=df_out, T_K=df_out['Temp (K) MELTS_Liq'],
P_kbar=5, Fe_FeNiCu_Sulf=0.65,
Fe3Fet_Liq=df_out['Fe3Fet_Liq'])

Smythe_CalcSulf.head()

Using inputted Fe_FeNiCu_Sulf ratio for calculations.
no non ideal SCSS as no Cu/CuFeNiCu

[4]:

	SCSS2_ppm_ideal_Smythe2017	SCSS2_ppm_ideal_Smythe2017_1sigma	T_Input_K	P_Input_kbar	Fe_FeNiCu_Sulf	Si_wt_atom	Ti_wt_atom	Al_wt_atom	Mg_wt_atom	Mn_wt_atom	Fe2_wt_atom	Ca_wt_atom	Na_wt_atom	K_wt_atom	P_wt_atom	H_wt_atom	Si_XA_ideal	Ti_XA_ideal	Al_XA_ideal	Mg_XA_ideal	Fe2_XA_ideal	Ca_XA_ideal	Na_XA_ideal	K_XA_ideal	H_XA_ideal	Si*Fe_ideal	Si_XA_non_ideal	Ti_XA_non_ideal	Al_XA_non_ideal	Mg_XA_non_ideal	Fe2_XA_non_ideal	Ca_XA_non_ideal	Na_XA_non_ideal	K_XA_non_ideal	H_XA_non_ideal	Si*Fe_non_ideal	log_SCSS_ideal	Fe_FeNiCu_Sulf_calc	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	H2O_Liq	Temp (K) MELTS_Liq	FeO_Liq	Fe2O3_Liq	H2O_Incom_Liq	Temp_HT1987_C_Liq	Factor_Liq	H2O_test_Liq	Sample_ID_Liq_Liq	Fe_FeNiCu_Sulf_calc
0	1006.245025	274.875727	1445.220313	5	0.65	0.482131	0.018332	0.149400	0.093565	0.001475	0.087091	0.110173	0.043725	0.005783	0.001971	0.006353	-13288.030247	-205.692099	-2756.471303	-1307.074423	-2984.966261	-862.748286	-579.220341	-167.791897	-111.154327	4894.578758	-13497.943762	-196.425413	-2838.589393	-1357.863277	-3039.060117	-973.005312	-599.594834	-165.301774	-112.875131	4946.976633	6.913981	0.65	51.456179	2.601690	13.529073	11.114610	0.185873	6.698477	10.974609	2.406926	0.483801	0.248535	0.101655	1445.220313	9.447747	1.852481	0.514405	1148.639387	1.000000	0.514405	0	0.65
1	998.862288	272.858987	1443.220313	5	0.65	0.482248	0.018470	0.150426	0.092240	0.001489	0.087339	0.109427	0.044117	0.005839	0.001991	0.006415	-13291.246596	-207.240432	-2775.399112	-1288.559744	-2993.474585	-856.902923	-584.413035	-169.417687	-112.231338	4909.718330	-13501.210920	-197.903992	-2858.081079	-1338.629174	-3047.722630	-966.412926	-604.970184	-166.903437	-113.968815	4962.278279	6.906617	0.65	51.458756	2.620771	13.619359	11.144152	0.187638	6.602326	10.898161	2.428038	0.488395	0.250895	0.102621	1443.220313	9.475545	1.854419	0.519548	1146.706750	1.009998	0.519548	1	0.65
2	991.146818	270.751353	1441.220313	5	0.65	0.482381	0.018619	0.151541	0.090800	0.001505	0.087604	0.108610	0.044546	0.005900	0.002011	0.006482	-13294.921234	-208.918471	-2795.977857	-1268.446550	-3002.550437	-850.505211	-590.088924	-171.197017	-113.410061	4925.965507	-13504.943607	-199.506433	-2879.272887	-1317.734445	-3056.962955	-959.197603	-610.845726	-168.656361	-115.165786	4978.699387	6.898863	0.65	51.462403	2.641448	13.717522	11.175642	0.189570	6.497934	10.814571	2.451116	0.493423	0.253478	0.103677	1441.220313	9.505299	1.856348	0.524889	1144.608472	1.020381	0.524889	2	0.65
3	988.661837	270.072532	1439.220313	5	0.65	0.482604	0.018845	0.152072	0.089578	0.001527	0.088188	0.107632	0.044952	0.005985	0.002041	0.006578	-13301.076921	-211.445793	-2805.768052	-1251.375396	-3022.555034	-842.848438	-595.464089	-173.640911	-115.076301	4961.080894	-13511.196537	-201.919896	-2889.354741	-1299.999958	-3077.330078	-950.562314	-616.409967	-171.063986	-116.857822	5014.190694	6.896352	0.65	51.469782	2.672548	13.761157	11.246506	0.192293	6.408435	10.713787	2.472653	0.500306	0.257120	0.105167	1439.220313	9.568634	1.864716	0.535182	1142.809538	1.040389	0.535182	3	0.65
4	995.268759	271.877343	1437.220313	5	0.65	0.482965	0.019201	0.151633	0.088700	0.001560	0.089316	0.106398	0.045312	0.006108	0.002085	0.006721	-13311.011669	-215.450181	-2797.678737	-1239.105910	-3061.222608	-833.185318	-600.243103	-177.224167	-117.582009	5028.300948	-13521.288226	-205.743881	-2881.024437	-1287.253718	-3116.698390	-939.664272	-621.357086	-174.594064	-119.402321	5082.130358	6.903013	0.65	51.481354	2.721741	13.714324	11.384440	0.196378	6.342291	10.585430	2.491197	0.510364	0.262582	0.107401	1437.220313	9.688901	1.884351	0.546507	1141.480047	1.062405	0.546507	4	0.65

Lets plot the ideal SCSS

[5]:

fig, (ax1) = plt.subplots(1, 1, figsize=(5,4.5), sharey=True)
ax1.plot(Smythe_CalcSulf['MgO_Liq'], Smythe_CalcSulf['SCSS2_ppm_ideal_Smythe2017'],
         '-r')

ax1.set_ylabel('SCSS (ppm)')
ax1.set_xlabel('FeO$_{T}$ Liq (Wt%)')

[5]:

Text(0.5, 0, 'FeO$_{T}$ Liq (Wt%)')

../../_images/Examples_Data_Input_Importing_Spreadsheet_8_1.png

Second example

Here we load measured glass contents to calculate the SCSS for each sample

[6]:

df_out2=ss.import_data('Glass_input_example.xlsx', sheet_name='Glass_input',
                       suffix="_Liq")
df_out2.head()

We have replaced all missing liquid oxides and strings with zeros.

[6]:

	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	Sample_ID_Liq	Cr2O3_Liq	Total_Liq	Sample_ID_Liq_Liq
0	50.822	2.056	13.235	13.339	0.252	6.631	11.356	2.490	0.247	0.189	H_1	0.04	100.7540	0
1	50.608	2.068	13.397	13.588	0.323	6.425	10.969	2.597	0.234	0.239	H_4	0.004	100.5429	1
2	50.427	2.081	13.276	13.806	0.231	6.516	11.222	2.577	0.232	0.176	H_7	0.046	100.6794	2
3	50.010	2.129	13.385	13.770	0.262	6.595	11.177	2.610	0.233	0.164	H_10	0.002	100.4291	3
4	49.588	2.065	13.120	13.099	0.237	6.459	10.832	2.593	0.227	0.222	H_13	0.031	98.5715	4

[7]:

Smythe_CalcSulf=ss.calculate_S2017_SCSS(df=df_out2, T_K=1400,
P_kbar=3, Fe_FeNiCu_Sulf=0.65,
Fe3Fet_Liq=0.15)

Smythe_CalcSulf.head()

Using inputted Fe_FeNiCu_Sulf ratio for calculations.
no non ideal SCSS as no Cu/CuFeNiCu

[7]:

	SCSS2_ppm_ideal_Smythe2017	SCSS2_ppm_ideal_Smythe2017_1sigma	T_Input_K	P_Input_kbar	Fe_FeNiCu_Sulf	Fe3Fet_Liq_input	Si_wt_atom	Ti_wt_atom	Al_wt_atom	Mg_wt_atom	Mn_wt_atom	Fe2_wt_atom	Fe3_wt_atom	Ca_wt_atom	Na_wt_atom	K_wt_atom	P_wt_atom	Si_XA_ideal	Ti_XA_ideal	Al_XA_ideal	Mg_XA_ideal	Fe2_XA_ideal	Ca_XA_ideal	Na_XA_ideal	K_XA_ideal	H_XA_ideal	Si*Fe_ideal	Si_XA_non_ideal	Ti_XA_non_ideal	Al_XA_non_ideal	Mg_XA_non_ideal	Fe2_XA_non_ideal	Ca_XA_non_ideal	Na_XA_non_ideal	K_XA_non_ideal	H_XA_non_ideal	Si*Fe_non_ideal	log_SCSS_ideal	Fe_FeNiCu_Sulf_calc	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	Fe3Fet_Liq	Sample_ID_Liq	Cr2O3_Liq	Total_Liq	Sample_ID_Liq_Liq	Fe_FeNiCu_Sulf_calc
0	1236.358668	337.735819	1400	3	0.65	0.15	0.476353	0.014492	0.146203	0.092655	0.002001	0.088873	0.015680	0.114041	0.045250	0.002953	0.001500	-13128.776773	-162.605276	-2697.483521	-1294.352927	-3046.048704	-893.037878	-599.418051	-85.694115	-0.0	4934.877695	-13336.174531	-155.279705	-2777.844304	-1344.647463	-3101.249502	-1007.165837	-620.503012	-84.422368	-0.0	4987.706982	7.119926	0.65	50.822	2.056	13.235	13.339	0.252	6.631	11.356	2.490	0.247	0.189	0.15	H_1	0.04	100.7540	0	0.65
1	1262.881353	344.981015	1400	3	0.65	0.15	0.475390	0.014608	0.148318	0.089974	0.002570	0.090731	0.016008	0.110397	0.047299	0.002804	0.001901	-13102.258153	-163.914179	-2736.508977	-1256.901601	-3109.736377	-864.501991	-626.551660	-81.362515	-0.0	5027.881257	-13309.236991	-156.529640	-2818.032368	-1305.740895	-3166.091330	-974.983136	-648.591066	-80.155052	-0.0	5081.706174	7.141151	0.65	50.608	2.068	13.397	13.588	0.323	6.425	10.969	2.597	0.234	0.239	0.15	H_4	0.004	100.5429	1	0.65
2	1300.631292	355.293158	1400	3	0.65	0.15	0.473234	0.014686	0.146837	0.091160	0.001836	0.092098	0.016249	0.112834	0.046889	0.002778	0.001398	-13042.825755	-164.785749	-2709.181782	-1273.476121	-3156.584995	-883.590034	-621.127756	-80.589429	-0.0	5080.476731	-13248.865729	-157.361945	-2789.891069	-1322.959449	-3213.788943	-996.510582	-642.976372	-79.393438	-0.0	5134.864698	7.170605	0.65	50.427	2.081	13.276	13.806	0.231	6.516	11.222	2.577	0.232	0.176	0.15	H_7	0.046	100.6794	2	0.65
3	1302.507628	355.805716	1400	3	0.65	0.15	0.469901	0.015043	0.148225	0.092379	0.002085	0.091972	0.016227	0.112521	0.047548	0.002793	0.001305	-12950.968052	-168.795183	-2734.803301	-1290.509920	-3152.247987	-881.135324	-629.859730	-81.036902	-0.0	5037.764881	-13155.556933	-161.190749	-2816.275878	-1340.655129	-3209.373339	-993.742167	-652.015499	-79.834271	-0.0	5091.695605	7.172047	0.65	50.010	2.129	13.385	13.770	0.262	6.595	11.177	2.610	0.233	0.164	0.15	H_10	0.002	100.4291	3	0.65
4	1230.690111	336.187341	1400	3	0.65	0.15	0.474535	0.014861	0.147972	0.092144	0.001921	0.089105	0.015721	0.111060	0.048110	0.002771	0.001799	-13078.693749	-166.742706	-2730.133948	-1287.224308	-3053.985553	-869.697883	-637.306360	-80.407242	-0.0	4928.861732	-13285.300336	-159.230738	-2811.467421	-1337.241848	-3109.330184	-980.843050	-659.724070	-79.213955	-0.0	4981.626616	7.115330	0.65	49.588	2.065	13.120	13.099	0.237	6.459	10.832	2.593	0.227	0.222	0.15	H_13	0.031	98.5715	4	0.65

Third example

say we have 2 phases, we then identify liquid using _Liq after each column heading

[10]:

df_out3=ss.import_data('Glass_input_example.xlsx', sheet_name='Glass_Ol_input')
df_out3.head()

We have replaced all missing liquid oxides and strings with zeros.

[10]:

	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	Sample_ID	Cr2O3_Liq	MgO_Ol	SiO2_Ol	FeO_Ol	Al2O3_Ol	CaO_Ol	MnO_Ol	NiO_Ol	Sample_ID_Liq
0	50.822	2.056	13.235	13.339	0.252	6.631	11.356	2.490	0.247	0.189	H_1	0.04	40.67610	39.50335	19.94265	0.02705	0.24615	0.29030	0.19135	0
1	50.608	2.068	13.397	13.588	0.323	6.425	10.969	2.597	0.234	0.239	H_4	0.004	40.16410	39.26485	21.20375	0.02400	0.23895	0.29335	0.18700	1
2	50.427	2.081	13.276	13.806	0.231	6.516	11.222	2.577	0.232	0.176	H_7	0.046	41.77670	39.36000	18.14420	0.03220	0.23040	0.25460	0.24260	2
3	50.010	2.129	13.385	13.770	0.262	6.595	11.177	2.610	0.233	0.164	H_10	0.002	41.93930	39.27305	18.17150	0.03355	0.22475	0.26455	0.24030	3
4	49.588	2.065	13.120	13.099	0.237	6.459	10.832	2.593	0.227	0.222	H_13	0.031	40.54345	39.10665	19.30270	0.02980	0.25095	0.27350	0.18230	4

[11]:

Smythe_CalcSulf=ss.calculate_S2017_SCSS(df=df_out3, T_K=1400,
P_kbar=3, Fe_FeNiCu_Sulf=0.65,
Fe3Fet_Liq=0.15)

Smythe_CalcSulf.head()

Using inputted Fe_FeNiCu_Sulf ratio for calculations.
no non ideal SCSS as no Cu/CuFeNiCu

[11]:

	SCSS2_ppm_ideal_Smythe2017	SCSS2_ppm_ideal_Smythe2017_1sigma	T_Input_K	P_Input_kbar	Fe_FeNiCu_Sulf	Fe3Fet_Liq_input	Si_wt_atom	Ti_wt_atom	Al_wt_atom	Mg_wt_atom	Mn_wt_atom	Fe2_wt_atom	Fe3_wt_atom	Ca_wt_atom	Na_wt_atom	K_wt_atom	P_wt_atom	Si_XA_ideal	Ti_XA_ideal	Al_XA_ideal	Mg_XA_ideal	Fe2_XA_ideal	Ca_XA_ideal	Na_XA_ideal	K_XA_ideal	H_XA_ideal	Si*Fe_ideal	Si_XA_non_ideal	Ti_XA_non_ideal	Al_XA_non_ideal	Mg_XA_non_ideal	Fe2_XA_non_ideal	Ca_XA_non_ideal	Na_XA_non_ideal	K_XA_non_ideal	H_XA_non_ideal	Si*Fe_non_ideal	log_SCSS_ideal	Fe_FeNiCu_Sulf_calc	SiO2_Liq	TiO2_Liq	Al2O3_Liq	FeOt_Liq	MnO_Liq	MgO_Liq	CaO_Liq	Na2O_Liq	K2O_Liq	P2O5_Liq	Fe3Fet_Liq	Sample_ID	Cr2O3_Liq	MgO_Ol	SiO2_Ol	FeO_Ol	Al2O3_Ol	CaO_Ol	MnO_Ol	NiO_Ol	Sample_ID_Liq	Fe_FeNiCu_Sulf_calc
0	1236.358668	337.735819	1400	3	0.65	0.15	0.476353	0.014492	0.146203	0.092655	0.002001	0.088873	0.015680	0.114041	0.045250	0.002953	0.001500	-13128.776773	-162.605276	-2697.483521	-1294.352927	-3046.048704	-893.037878	-599.418051	-85.694115	-0.0	4934.877695	-13336.174531	-155.279705	-2777.844304	-1344.647463	-3101.249502	-1007.165837	-620.503012	-84.422368	-0.0	4987.706982	7.119926	0.65	50.822	2.056	13.235	13.339	0.252	6.631	11.356	2.490	0.247	0.189	0.15	H_1	0.04	40.67610	39.50335	19.94265	0.02705	0.24615	0.29030	0.19135	0	0.65
1	1262.881353	344.981015	1400	3	0.65	0.15	0.475390	0.014608	0.148318	0.089974	0.002570	0.090731	0.016008	0.110397	0.047299	0.002804	0.001901	-13102.258153	-163.914179	-2736.508977	-1256.901601	-3109.736377	-864.501991	-626.551660	-81.362515	-0.0	5027.881257	-13309.236991	-156.529640	-2818.032368	-1305.740895	-3166.091330	-974.983136	-648.591066	-80.155052	-0.0	5081.706174	7.141151	0.65	50.608	2.068	13.397	13.588	0.323	6.425	10.969	2.597	0.234	0.239	0.15	H_4	0.004	40.16410	39.26485	21.20375	0.02400	0.23895	0.29335	0.18700	1	0.65
2	1300.631292	355.293158	1400	3	0.65	0.15	0.473234	0.014686	0.146837	0.091160	0.001836	0.092098	0.016249	0.112834	0.046889	0.002778	0.001398	-13042.825755	-164.785749	-2709.181782	-1273.476121	-3156.584995	-883.590034	-621.127756	-80.589429	-0.0	5080.476731	-13248.865729	-157.361945	-2789.891069	-1322.959449	-3213.788943	-996.510582	-642.976372	-79.393438	-0.0	5134.864698	7.170605	0.65	50.427	2.081	13.276	13.806	0.231	6.516	11.222	2.577	0.232	0.176	0.15	H_7	0.046	41.77670	39.36000	18.14420	0.03220	0.23040	0.25460	0.24260	2	0.65
3	1302.507628	355.805716	1400	3	0.65	0.15	0.469901	0.015043	0.148225	0.092379	0.002085	0.091972	0.016227	0.112521	0.047548	0.002793	0.001305	-12950.968052	-168.795183	-2734.803301	-1290.509920	-3152.247987	-881.135324	-629.859730	-81.036902	-0.0	5037.764881	-13155.556933	-161.190749	-2816.275878	-1340.655129	-3209.373339	-993.742167	-652.015499	-79.834271	-0.0	5091.695605	7.172047	0.65	50.010	2.129	13.385	13.770	0.262	6.595	11.177	2.610	0.233	0.164	0.15	H_10	0.002	41.93930	39.27305	18.17150	0.03355	0.22475	0.26455	0.24030	3	0.65
4	1230.690111	336.187341	1400	3	0.65	0.15	0.474535	0.014861	0.147972	0.092144	0.001921	0.089105	0.015721	0.111060	0.048110	0.002771	0.001799	-13078.693749	-166.742706	-2730.133948	-1287.224308	-3053.985553	-869.697883	-637.306360	-80.407242	-0.0	4928.861732	-13285.300336	-159.230738	-2811.467421	-1337.241848	-3109.330184	-980.843050	-659.724070	-79.213955	-0.0	4981.626616	7.115330	0.65	49.588	2.065	13.120	13.099	0.237	6.459	10.832	2.593	0.227	0.222	0.15	H_13	0.031	40.54345	39.10665	19.30270	0.02980	0.25095	0.27350	0.18230	4	0.65

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