geoelectrics: 3D-Visualization of Geoelectric Resistivity Measurement Profiles

Description

Electrical resistivity tomography is an efficient geophysical technique to investigate the spatial extent of subsurface structures. Many scientific objectives in geology demand three-dimensional imaging. 3D electrical resistivity tomography provides a technique to survey three-dimensional structures. Nonetheless, 3D electrical resistivity tomography requires an enormous amount of time as well as a high work load. In most cases, 2D electrical resistivity tomography is used to obtain two-dimensional subsurface profiles. This R package enables the user to visualize two-dimensional profiles in three dimensions.

Author(s)

Anja Kleebaum

See Also

Useful links:

• https://github.com/kleebaum/geoelectrics

• Report bugs at https://github.com/kleebaum/geoelectrics/issues

Examples

library(geoelectrics)
demo(geoelectrics)

GPS Coordinates Class

Description

A class to handle gps coordinates.

Slots

address

address of the gps ascii file

exact

data frame that contains measured gps coordinates

relative

relative coordinates, normalized to (0,0)

lm

linear model of the measured gps coordinates

lmRelative

linear model of relative coordinates

See Also

Profile-class, ProfileSet-class, adjustHeight, calcRelativeCoords

Examples

gpsCoordinates = new('GpsCoordinates', address = system.file('extdata/gps/p1.txt',
                 package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[1]]@gpsCoordinates
sinkhole@profiles[[1]]@gpsCoordinates@address
sinkhole@profiles[[1]]@gpsCoordinates@exact
sinkhole@profiles[[1]]@gpsCoordinates@lm
sinkhole@profiles[[1]]@gpsCoordinates@relative
sinkhole@profiles[[1]]@gpsCoordinates@lmRelative

Processed Data Class

Description

A class to handle processed geoelectrics data in ascii format. The processed data class parses .xyz files produced by the software Res2DInv. If you want to use another format, overwrite the parseProcessedDataFile method.

Slots

address

address of the processed ascii file

points

data frame that contains positions and values withouth topography information

pointsWithTopo

data frame that contains positions and values with topography information

height

data frame that contains topography information (distances and heights). It is reconstructed from .xyz-file.

minData

minimum value

maxData

maximum value

See Also

parseProcessedDataFile, Profile-class, ProfileSet-class

Examples

processedData = new('ProcessedData',
                     address = system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                     package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[1]]@processedData
sinkhole@profiles[[1]]@processedData@points
sinkhole@profiles[[1]]@processedData@pointsWithTopo
sinkhole@profiles[[1]]@processedData@height
sinkhole@profiles[[1]]@processedData@minData
sinkhole@profiles[[1]]@processedData@maxData

Profile Class

Description

A class to handle a single profile.

Slots

title

title of the profile (e.g. Profile 1).

number

index of the profile.

processedData

object of Processed Data Class (ProcessedData-class).

rawData

object of Raw Data Class (RawData-class).

measurementType

type of measurement (e.g. Dipole Dipole, Wenner, ...).

gpsCoordinates

object of GpsCoordinates Class (GpsCoordinates-class).

See Also

ProcessedData-class, RawData-class, GpsCoordinates-class, plot3d, plot

Examples

p1 <- new('Profile',
           title = 'Profile 1',
           processedData =
             new('ProcessedData', address = system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                                      package='geoelectrics')),
           rawData =
             new('RawData', address = system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
                                      package='geoelectrics')),
           measurementType = 'DipoleDipole',
           gpsCoordinates =
             new('GpsCoordinates', address = system.file('extdata/gps/p1.txt',
                                             package='geoelectrics')))

p1@title
p1@processedData
p1@rawData
p1@measurementType
p1@gpsCoordinates

plot3d(p1)

Profile Set Class

Description

A class to handle a collection of many profiles.

Slots

title

title to plot

profiles

list that contains objects of class Profile (Profile-class)

minLat

minimum latitude value of all profiles

minLon

minimum longitude value of all profiles

minData

minimum data value of all profiles

maxData

maximum data value of all profiles

See Also

Profile-class, plot3d

Examples

# sinkhole <- new('ProfileSet',
#                profiles = list(p1, p2, p3),
#                title='Sinkhole')

data(sinkhole)
plot3d(sinkhole)

Raw Data Class

Description

A class to handle geoelectrics raw data. The raw data class parses .dat files provided by the GeoTest software by Dr. Rauen. If you want to use another format, overwrite the parseRawDataFile method.

Slots

address

address of the raw data ascii file.

points

data frame that contains raw data resistance values and their positions (distance and depth).

See Also

parseRawDataFile, Profile-class, ProfileSet-class

Examples

rawData = new('RawData', address = system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
          package='geoelectrics'))

data(sinkhole)
sinkhole@profiles[[2]]@rawData
sinkhole@profiles[[2]]@rawData@address
sinkhole@profiles[[2]]@rawData@points

Adjust Profile Height

Description

Adjusts the height of a single profile (adds a delta value to ALL data points). This is necessary if GPS measurement heights of two profiles differ systematically.

Usage

adjustHeight(object, delta)

## S4 method for signature 'Profile'
adjustHeight(object, delta)

Arguments

Value

adjusted profile

See Also

GpsCoordinates-class, Profile-class

Examples

p3 <- new(
  "Profile",
  title = "Profile 3",
  processedData =
    new("ProcessedData",
        address = system.file("extdata/processed/p3_DipolDipol_S-N.xyz",
                  package='geoelectrics')),
  rawData =
    new("RawData",
        address = system.file("extdata/raw/p3_DipolDipol_S-N.dat",
                  package='geoelectrics')),
  measurementType = "DipolDipol",
  gpsCoordinates =
    new("GpsCoordinates",
        address = system.file("extdata/gps/p3.txt",
                  package='geoelectrics'))
)

p3 <- adjustHeight(p3, -10)

Calculate Relative Coordinates

Description

Calculates relative coordinates (unity: meters) from GPS coordinates (either given in UTM or Gauss Krueger). This method is used when a profile set of many profiles is instantiated.

Usage

calcRelativeCoords(coords, minLat, minLon)

Arguments

Value

data frame that contains the relative coordinates (latitude and longitude).

See Also

ProfileSet-class, GpsCoordinates-class

Graphical User Interface of the Geoelectrics R Package

Description

This method starts a simple TclTk graphical user interface (GUI) provided by this package.

Usage

geoelectricsGui()

Examples

# geoelectricsGui()

Gets the Height Information for a Profile

Description

Returns the heights for certain distances along the profile (topography information).

Usage

getHeightInformation(object)

## S4 method for signature 'ProcessedData'
getHeightInformation(object)

Arguments

Value

data frame containing distances and heights along the profile

See Also

GpsCoordinates-class, Profile-class, ProcessedData-class

Examples

data(sinkhole)

getHeightInformation(sinkhole@profiles[[1]]@processedData)

Levelplot of Geoelectrics Data

Description

Plots the interpolated resistance values of the geoelectrics data.

Usage

levelplot(x, data, ...)

## S4 method for signature 'Profile'
levelplot(x, dataType = "processed",
  withTopo = FALSE, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title), col = colors, breaks = 18, trafo = log,
  backtrafo = exp, aspect = "iso", ...)

## S4 method for signature 'ProfileSet'
levelplot(x, dataType = "processed",
  withTopo = FALSE, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title), col = colors, breaks = 18, trafo = log,
  backtrafo = exp, aspect = "iso", ...)

levelplotProcessedData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), col = colors,
  breaks = 18, trafo = log, backtrafo = exp, aspect = "iso", ...)

levelplotProcessedDataWithTopo(x, xlab = "Length [m]",
  ylab = "Height [m]", main = paste(x@title, "with topography"),
  col = colors, breaks = 18, trafo = log, backtrafo = exp,
  aspect = "iso", ...)

levelplotRawData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography (raw data)"), col = colors,
  trafo = log, aspect = "iso", ...)

Arguments

See Also

Profile-class

Examples

data(sinkhole)

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'raw')
levelplotLegendLabel()

Levelplot Legend Label

Description

Plots the label of the levelplot.

Usage

levelplotLegendLabel(legend.lab = "Resistivity",
  unit = expression(paste("[", Omega, "m]")))

Arguments

See Also

levelplot

Examples

data(sinkhole)

levelplot(sinkhole@profiles[[1]])
levelplotLegendLabel()

levelplot(sinkhole@profiles[[2]])
levelplotLegendLabel()

levelplot(sinkhole@profiles[[3]])
levelplotLegendLabel()

Maps color to resistivity value

Description

Maps color to (resistivity) values. A minimum and maximum value can be specified.

Usage

myColorRamp(col, values, minData = min(values), maxData = max(values))

Arguments

Parses a Processed Data File

Description

Parses .xyz files produced by the software Res2DInv. Needs to be overwritten if another processed data format is used.

Usage

parseProcessedDataFile(address, skip = 0)

Arguments

Value

list of two data frames: The first data frame contains points without topography (distance, depth and resistivity values). The second data frame contains points with topography (distance, height and resistivity values).

See Also

ProcessedData-class, Profile-class

Examples

fileAddress <- system.file('extdata/processed/p1_DipolDipol_SW-NE.xyz',
                   package = 'geoelectrics')

processedData = new('ProcessedData')
processedData@address = fileAddress
processedData@points <- parseProcessedDataFile(address = fileAddress)[[1]]
processedData@pointsWithTopo <- parseProcessedDataFile(address = fileAddress)[[2]]

Parses a Raw Data File

Description

Parses a geoelectrics raw data file created by the GeoTest software by Dr. Rauen. Needs to be overwritten if another raw data format is used.

Usage

parseRawDataFile(address, skip = 9)

Arguments

Value

data frame containing distance, depth and resistivity values

See Also

RawData-class, Profile-class

Examples

fileAddress <- system.file('extdata/raw/p1_DipolDipol_SW-NE.dat',
                   package = 'geoelectrics')
                   
rawData = new('RawData')
rawData@address = fileAddress
rawData@points <- parseRawDataFile(address = fileAddress)

Plot Geoelectrics Data Points

Description

Plots the geoelectrics data points of a profile.

Usage

## S4 method for signature 'Profile,ANY'
plot(x, dataType = "processed", withTopo = T,
  xlab = "Length [m]", ylab = "Height [m]", main = paste(x@title,
  "with topography"), asp = 1, ...)

## S4 method for signature 'ProfileSet,ANY'
plot(x, dataType = "processed",
  withTopo = T, xlab = "Length [m]", ylab = "Height [m]",
  main = paste(x@title, "with topography"), asp = 1, ...)

plotProcessedData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), ...)

plotProcessedDataWithTopo(x, xlab = "Length [m]", ylab = "Height [m]",
  main = paste(x@title, "with topography"), ...)

plotRawData(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "without topography"), ...)

plotRawDataWithTopo(x, xlab = "Length [m]", ylab = "Depth [m]",
  main = paste(x@title, "with topography"),
  height = x@processedData@height, spline = TRUE, ...)

Arguments

See Also

Profile-class, plot3d, levelplot

Examples

data(sinkhole)

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
plotProcessedData(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
plotProcessedDataWithTopo(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = FALSE)
plotRawData(sinkhole@profiles[[1]])

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = TRUE)
plotRawDataWithTopo(sinkhole@profiles[[1]])

3D Scatterplot of Geoelectrics Profiles

Description

Plots the interpolated resistance values of the processed data for a single profile or a set of profiles.

Usage

## S4 method for signature 'ProfileSet'
plot3d(x, title = x@title, sub = "",
  xlab = "", ylab = "", zlab = "", minData = x@minData,
  maxData = x@maxData, col = colors, trafo = log,
  psize = pointsize, ...)

## S4 method for signature 'Profile'
plot3d(x, title = "", sub = "", xlab = "",
  ylab = "", zlab = "", minData = x@processedData@minData,
  maxData = x@processedData@maxData, col = colors, trafo = log,
  psize = pointsize, ...)

Arguments

See Also

Profile-class, ProfileSet-class, plot, levelplot

Examples

data(sinkhole)

plot3d(sinkhole@profiles[[1]])
plot3d(sinkhole)

Plot Profile Intersection

Description

Plots resistivity against height on and next to the intersection line between two profiles.

Usage

plotIntersect(.Object1, .Object2 = NULL,
  xlab = "Height above sea level [m]",
  ylab = expression(paste("Resistivity [", Omega, "m]")), main = "",
  trafo = log, backtrafo = exp, col = colors, pch = c(20, 20),
  type = "p", legendLoc = "bottomleft")

## S4 method for signature 'ProfileSet,ANY'
plotIntersect(.Object1, xlab, ylab, main, trafo,
  backtrafo, col, pch, type, legendLoc)

## S4 method for signature 'Profile,Profile'
plotIntersect(.Object1, .Object2 = NULL,
  xlab = "Height above sea level [m]",
  ylab = expression(paste("Resistivity [", Omega, "m]")), main = "",
  trafo = log, backtrafo = exp, col = colors, pch = c(20, 20),
  type = "p", legendLoc = "bottomleft")

Arguments

See Also

ProfileSet-class

Examples

data(sinkhole)

plotIntersect(sinkhole)
plotIntersect(sinkhole@profiles[[1]], sinkhole@profiles[[2]])

Plots Legend

Description

Plots the legend for resistivity values.

Usage

plotLegend(.Object, legend.lab = expression(paste("Resistivity [", Omega,
  " m]")), minData = 0, maxData = 999999, breaks = NULL,
  legend.line = 2.2, nlevel = 18, lab.breaks = c(), horizontal = T,
  col = colors, trafo = log, backtrafo = exp, ...)

## S4 method for signature 'ProfileSet'
plotLegend(.Object, legend.lab,
  minData = .Object@minData, maxData = .Object@maxData)

## S4 method for signature 'Profile'
plotLegend(.Object, legend.lab,
  minData = .Object@processedData@minData,
  maxData = .Object@processedData@maxData)

Arguments

See Also

Profile-class, ProfileSet-class, plot3d,

Examples

data(sinkhole)

plotLegend(sinkhole)

# for linear scale:
plotLegend(sinkhole@profiles[[1]],
           trafo=function(x) x,
           backtrafo=function(x) x,
           minData=100, maxData=50000)

Filled Sinkhole

Description

Geoelectrics profiles measured at a filled sinkhole. This data set contains an object of the ProfileSet class.

Format

Object of Profile Set class including three Profiles.

See Also

ProfileSet-class, Profile-class, plot3d, plot, levelplot, plotLegend, plotIntersect

Examples

data(sinkhole)

# Plot the processed data in three dimensions
plot3d(sinkhole)

# Plot legend for the profile set
plot.new()
plotLegend(sinkhole)

# Plot raw data of profile 1
plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = FALSE, 
     main = 'Profile 1', ylab = 'Depth [m]')

plot(sinkhole@profiles[[1]], dataType = 'raw', withTopo = TRUE)

levelplot(sinkhole@profiles[[1]], dataType = 'raw')
levelplotLegendLabel()

# Plot processed data of profile 1
plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE,
     main = 'Profile 1', ylab = 'Depth [m]')

plot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = FALSE)
levelplotLegendLabel()

levelplot(sinkhole@profiles[[1]], dataType = 'processed', withTopo = TRUE)
levelplotLegendLabel()

# Compare processed data values on the intersection line between two profiles
plotIntersect(sinkhole)