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Read EPR Simulation Parameters and Information from MATLAB .mat File

Source: R/readMAT_params_file.R
readMAT_params_file.Rd

Function is based on the readMat and provides the reading of a .mat simulation file content from EasySpin MATLAB, including structures/variables and fields. It can be also used to read and store simulated EPR spectrum in the form of R data frame (see Examples).

Usage

readMAT_params_file(path_to_MAT, str.var = NULL, field.var = NULL)

Arguments

path_to_MAT

Character string, path to .mat MATLAB file with all variables saved in workspace. The file path can be also defined by file.path.

str.var

Character string, structure/variable, which may contain fields, such as Sys and g => Sys.g, respectively. Default: str.var = NULL.

field.var

Character string, field variable after 'dot', which is available only for certain structures/variables, see e.g. example above (Sys.g), therefore the default value is NULL and the string is applied only for structures with fields.

Value

Unless the str.var and/or field.var are not specified, the output is list with all original parameters/structures from MATLAB file. Otherwise, the function returns either numeric/character vector/value or list depending on class of the original parameter/field variable.

See also

Other Data Reading: readEPR_Exp_Specs(), readEPR_Exp_Specs_kin(), readEPR_Exp_Specs_multif(), readEPR_Sim_Spec(), readEPR_param_slct(), readEPR_params_slct_kin(), readEPR_params_slct_quant(), readEPR_params_slct_sim(), readEPR_params_tabs(), readEPR_solvent_props()

Examples

## loading the package built-in
## `Aminoxyl_radical_a.mat` file as an example
aminoxyl.mat.file <-
  load_data_example(file = "Aminoxyl_radical_a.mat")
#
## reading the entire `mat` file as list
## and assign variable
aminoxyl.mat.list <-
  readMAT_params_file(aminoxyl.mat.file)
#
## read the `Sim1` structure/variable content into list
aminoxyl.mat.sim1 <-
  readMAT_params_file(aminoxyl.mat.file,
                      str.var = "Sim1")
#
## list preview
aminoxyl.mat.sim1
#> $g
#> [1] 2.007017
#> 
#> $Nucs
#> [1] "14N"
#> 
#> $n
#> [1] 1
#> 
#> $A
#> [1] 52.324276
#> 
#> $lwpp
#> [1] 0.4400000 0.1008846
#> 
#
## compare the previous simulation parameters with
## those obtained by the `eval_sim_EPR_isoFit()`
## function (look at the corresponding examples)
#
## alternatively the `Sim1` (its dimension > 2)
## can be also read by the following command
## however, the returned output has a complex
## array-list structure
aminoxyl.mat.list$Sim1[, , 1]
#> $g
#>          [,1]
#> [1,] 2.007017
#> 
#> $Nucs
#>      [,1] 
#> [1,] "14N"
#> 
#> $n
#>      [,1]
#> [1,]    1
#> 
#> $A
#>           [,1]
#> [1,] 52.324276
#> 
#> $lwpp
#>      [,1]      [,2]
#> [1,] 0.44 0.1008846
#> 
#
## read the `Sim1` structure/variable
## and the field `Nucs` corresponding to nuclei
## considered in the EPR simulation
aminoxyl.mat.sim1.nucs <-
  readMAT_params_file(aminoxyl.mat.file,
                      str.var = "Sim1",
                      field.var = "Nucs")
#
## preview
aminoxyl.mat.sim1.nucs
#> [1] "14N"
#
## reading the magnetic flux density
## `B` column/vector corresponding to simulated
## and experimental EPR spectrum
aminoxyl.B.G <-
  readMAT_params_file(aminoxyl.mat.file,
                      str.var = "B")
#
## preview of the first 6 values
aminoxyl.B.G[1:6]
#> [1] 3332.7000 3332.9005 3333.1009 3333.3014 3333.5019 3333.7023
#
## reading the intensity related to simulated
## EPR spectrum
aminoxyl.sim.fitSpec <-
  readMAT_params_file(aminoxyl.mat.file,
                      str.var = "fit1",
                      field.var = "fitSpec")
#
## preview of the first 6 values
aminoxyl.sim.fitSpec[1:6]
#> [1] 0.00068169341 0.00066601473 0.00047674618 0.00015739402 0.00020037360
#> [6] 0.00016455010
#
## The last two examples can be used
## to load the simulated EPR spectrum
## by the `EasySpin` from `mat` file =>
simulation.aminoxyl.spectr.df <-
  data.frame(Bsim_G = aminoxyl.B.G,
             dIeprSim_over_dB = aminoxyl.sim.fitSpec)
#
## preview
head(simulation.aminoxyl.spectr.df)
#>      Bsim_G dIeprSim_over_dB
#> 1 3332.7000    0.00068169341
#> 2 3332.9005    0.00066601473
#> 3 3333.1009    0.00047674618
#> 4 3333.3014    0.00015739402
#> 5 3333.5019    0.00020037360
#> 6 3333.7023    0.00016455010