Accessor

petropandas.pandas_accessors.OxidesAccessor

Use .oxides pandas dataframe accessor.

props property

Returns properties.

oxwt(**kwargs)

Convert molar proportions to oxides weight percents.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with oxides weight percents

cat_number(**kwargs)

Calculate cations number.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with cations numbers

oxy_number(**kwargs)

Calculate oxygens number.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with oxygens numbers

omega(**kwargs)

Oxygen to positive atomic charges ratio

Parameters:

Name	Type	Description	Default
mineral	Mineral	noxy and ncat are taken from Mneral instance	required
noxy	int	ideal number of oxygens. Default 1	required
ncat	int	ideal number of cations. Default 1	required

onf(noxy)

Oxygen normalisation factor - ideal oxygens / sum of oxygens

Other Parameters:

Name	Type	Description
noxy	int	ideal oxygens

Returns:

Type	Description
Series	pandas.Series: oxygen normalisation factors

cnf(ncat)

Cation normalisation factor - ideal cations / sum of cations

Parameters:

Name	Type	Description	Default
ncat	int	ideal cations	required

Returns:

Type	Description
Series	pandas.Series: cation normalisation factors

cations(**kwargs)

Cations calculated on the basis of oxygens or cations.

Other Parameters:

Name	Type	Description
noxy	int	ideal number of oxygens. Default 1
ncat	int	ideal number of cations. Default 1
tocat	bool	when True normalized to ncat, otherwise to noxy. Default False

Returns:

Type	Description
DataFrame	Dataframe with calculated cations

charges(ncat, **kwargs)

Calculates charges based on number of cations.

Parameters:

Name	Type	Description	Default
ncat	int	number of cations	required

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included.Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with charges

charge_def(**kwargs)

Calculates charge deficiency based on number of oxygens and cations.

Other Parameters:

Name	Type	Description
mineral	Mineral	noxy and ncat are taken from Mneral instance
noxy	int	ideal number of oxygens. Default 1
ncat	int	ideal number of cations. Default 1

Returns:

Type	Description
Series	pandas.Series: Charge deficiency

apatite_correction(**kwargs)

Apatite correction

Note

All P2O5 is assumed to be apatite based and is removed from composition

CaO mol% = CaO mol% - (10 / 3) * P2O5 mol%

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Apatite corrected dataframe

convert_Fe(**kwargs)

Recalculate FeO to Fe2O3 or vice-versa.

Note

When only FeO exists, all is recalculated to Fe2O3. When only Fe2O3 exists, all is recalculated to FeO. When both exists, Fe2O3 is recalculated and added to FeO. Otherwise datatable is not changed.

Other Parameters:

Name	Type	Description
to	str	to what iron oxide Fe should be converted. Default "FeO"
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with converted Fe oxide

recalculate_Fe(**kwargs)

Recalculate Fe based on charge balance.

Note

Either both FeO and Fe2O3 are present or any of then, the composition is modified to fullfil charge balance for given cations and oxygens.

Number of cations and oxygens could be provided by ncat and noxy args or by Mineral instance

Other Parameters:

Name	Type	Description
mineral	Mineral	noxy and ncat are taken from Mneral instance
noxy	int	ideal number of oxygens. Default 1
ncat	int	ideal number of cations. Default 1
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with recalculated Fe

apfu(mineral, **kwargs)

Calculate a.p.f.u for given mineral

Parameters:

Name	Type	Description	Default
mineral	Mineral	Mineral instance (see petropandas.minerals)	required

Other Parameters:

Name	Type	Description
force	bool	when True, remaining cations are added to last site
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with apfu for given mineral

check_stechiometry(mineral, **kwargs)

Calculate average missfit of populated and ideal cations on sites for given mineral

Parameters:

Name	Type	Description	Default
mineral	Mineral	Mineral instance (see petropandas.minerals)	required

Other Parameters:

Name	Type	Description
force	bool	when True, remaining cations are added to last site

Returns:

Type	Description
Series	Series with calculated misfit

endmembers(mineral, **kwargs)

Calculate endmembers proportions

Parameters:

Name	Type	Description	Default
mineral	Mineral	Mineral instance (see petropandas.minerals)	required

Other Parameters:

Name	Type	Description
tocat	bool	when True normalize to cations, otherwise to oxygens. Default False
force	bool	when True, remaining cations are added to last site
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with calculated endmembers

TCbulk(**kwargs)

Print oxides formatted as THERMOCALC bulk script

Note

The CaO is recalculate using apatite correction based on P205 if available.

Other Parameters:

Name	Type	Description
H2O	float	wt% of water. When -1 the amount is calculated as 100 - Total. Default -1.
oxygen	float	value to calculate moles of ferric iron. Moles FeO = FeOtot - 2O and moles Fe2O3 = O. Default 0.01
system	str	axfile to be used. One of 'MnNCKFMASHTO', 'NCKFMASHTO', 'KFMASH', 'NCKFMASHTOCr', 'NCKFMASTOCr'. Default 'MnNCKFMASHTO'

Perplexbulk(**kwargs)

Print oxides formatted as PerpleX thermodynamic component list

Note

The CaO is recalculate using apatite correction based on P205 if available.

Other Parameters:

Name	Type	Description
H2O	float	wt% of water. When -1 the amount is calculated as 100 - Total. Default -1.
oxygen	float	value to calculate moles of ferric iron. Moles FeO = FeOtot - 2O and moles Fe2O3 = O. Default 0.01
system	str	system to be used. One of 'MnNCKFMASHTO', 'NCKFMASHTO', 'KFMASH', 'NCKFMASHTOCr', 'NCKFMASTOCr'. Default 'MnNCKFMASHTO'

MAGEMin(**kwargs)

Print oxides formatted as MAGEMin bulk file

Note

The CaO is recalculate using apatite correction based on P205 if available.

Other Parameters:

Name	Type	Description
H2O	float	wt% of water. When -1 the amount is calculated as 100 - Total. Default -1.
oxygen	float	value to calculate moles of ferric iron. Moles FeO = FeOtot - 2O and moles Fe2O3 = O. Default 0.01
db	str	MAGEMin database. 'mp' metapelite (White et al. 2014), 'mb' metabasite (Green et al. 2016), 'ig' igneous (Holland et al. 2018), 'um' ultramafic (Evans & Frost 2021), 'ume' ultramafic extended (Evans & Frost 2021 + pl, hb and aug from Green et al. 2016), 'mpe' Metapelite extended (White et al. 2014, Green et al. 2016, Evans & Frost 2021), 'mbe' Metabasite extended (Green et al. 2016, Diener et al. 2007), 'mtl' mantle (Holland et al. 2013). Default is "mp"
sys_in	str	system comp "wt" or "mol". Default is "mol"
title	str	used as title. Default index
comment	str	used as comment. Default 'petropandas'

df(**kwargs)

Returns dataframe.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe

dropna(**kwargs)

Drop columns with NA values.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].

Returns:

Type	Description
DataFrame	Dataframe without NA columns

molprop(**kwargs)

Convert oxides weight percents to molar proportions.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with molar proportions

mean()

Return Dataframe with single row of arithmetic means of valid columns

sum()

Return Dataframe with single row of sum of valid columns

scale(**kwargs)

Normalize values to given sum.

Other Parameters:

Name	Type	Description
to	float	Sum of values. Default 100.0
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Scaled dataframe

plot(**kwargs)

Paiplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

boxplot(**kwargs)

Boxplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

heatmap(**kwargs)

Correlation heatmap of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

petropandas.pandas_accessors.IonsAccessor

Use .ions pandas dataframe accessor.

props property

Returns properties.

wt(omega=1)

Oxides weight percents calculated from ions.

Returns:

Type	Description
DataFrame	Dataframe with calculated oxides weight percents

df(**kwargs)

Returns dataframe.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe

dropna(**kwargs)

Drop columns with NA values.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].

Returns:

Type	Description
DataFrame	Dataframe without NA columns

molprop(**kwargs)

Convert oxides weight percents to molar proportions.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with molar proportions

mean()

Return Dataframe with single row of arithmetic means of valid columns

sum()

Return Dataframe with single row of sum of valid columns

scale(**kwargs)

Normalize values to given sum.

Other Parameters:

Name	Type	Description
to	float	Sum of values. Default 100.0
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Scaled dataframe

plot(**kwargs)

Paiplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

boxplot(**kwargs)

Boxplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

heatmap(**kwargs)

Correlation heatmap of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

petropandas.pandas_accessors.ElementsAccessor

Use .elements pandas dataframe accessor.

props property

Returns properties.

df(**kwargs)

Returns dataframe.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe

dropna(**kwargs)

Drop columns with NA values.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].

Returns:

Type	Description
DataFrame	Dataframe without NA columns

molprop(**kwargs)

Convert oxides weight percents to molar proportions.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with molar proportions

mean()

Return Dataframe with single row of arithmetic means of valid columns

sum()

Return Dataframe with single row of sum of valid columns

scale(**kwargs)

Normalize values to given sum.

Other Parameters:

Name	Type	Description
to	float	Sum of values. Default 100.0
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Scaled dataframe

plot(**kwargs)

Paiplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

boxplot(**kwargs)

Boxplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

heatmap(**kwargs)

Correlation heatmap of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

petropandas.pandas_accessors.REEAccessor

Use .ree pandas dataframe accessor.

props property

Returns properties.

normalize(**kwargs)

Normalize REE by reservoir.

Note

Predefined reservoirs are imported from GERM Reservoir Database. You can check all available reservoirs in config["reservoirs"].

Other Parameters:

Name	Type	Description
reservoir	str	Name of reservoir. Deafult "CI Chondrites"
reference	str	Reference. Default "McDonough & Sun 1995"
source	str	Original source. Deafult same as reference.
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with normalized REE composition

plot(**kwargs)

Spiderplot of REE data.

Note

List of REE used for plot could be set in config["ree_plot"]

Other Parameters:

Name	Type	Description
grouped	bool	When True aggegated data with confidence interval is drawn. Default False
boxplot	bool	When True, boxplot for each REE is drawn. Default False
boxplot_props	dict	Additional arguments passed to sns.boxplot. Default {"color": "grey"}.
hue	str or None	Name of columns used for colors.
palette	string, list, dict, or matplotlib.colors.Colormap	Method for choosing the colors to use when mapping the hue semantic.
legend	"auto", "brief", "full", or False	How to draw the legend.
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

df(**kwargs)

Returns dataframe.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe

dropna(**kwargs)

Drop columns with NA values.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].

Returns:

Type	Description
DataFrame	Dataframe without NA columns

molprop(**kwargs)

Convert oxides weight percents to molar proportions.

Other Parameters:

Name	Type	Description
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Dataframe with molar proportions

mean()

Return Dataframe with single row of arithmetic means of valid columns

sum()

Return Dataframe with single row of sum of valid columns

scale(**kwargs)

Normalize values to given sum.

Other Parameters:

Name	Type	Description
to	float	Sum of values. Default 100.0
keep	list	list of additional columns to be included. Default [].
dropna	bool	whether to drop columns with NA only. Default True

Returns:

Type	Description
DataFrame	Scaled dataframe

boxplot(**kwargs)

Boxplot of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.

heatmap(**kwargs)

Correlation heatmap of data.

All keywords except further listed are passed to seaborn pairplot.

Use all accessor valid columns or columns provided in vars

Other Parameters:

Name	Type	Description
title	str	Title of the plot. Default None
filename	str	If not none, plot is saved to file. Default None.
dpi	int	DPI used for savefig. Default 150.