| Title: | Analytical Tools for Radiation Oncology |
|---|---|
| Description: | Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data. |
| Authors: | Reid F. Thompson [aut, cre] |
| Maintainer: | Reid F. Thompson <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1.9 |
| Built: | 2025-01-22 07:00:13 UTC |
| Source: | https://github.com/cran/RadOnc |
Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
The DESCRIPTION file:
| Package: | RadOnc |
| Type: | Package |
| Title: | Analytical Tools for Radiation Oncology |
| Version: | 1.1.9 |
| Date: | 2025-01-21 |
| Authors@R: | person(given = c("Reid", "F."), family = "Thompson", role = c("aut", "cre"), email = "[email protected]") |
| Imports: | stats, utils |
| Depends: | R (>= 3.0.0), graphics, grDevices, methods, oro.dicom (>= 0.5.0), ptinpoly |
| Description: | Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data. |
| License: | GPL (>= 2) |
| LazyData: | yes |
| LazyLoad: | yes |
| NeedsCompilation: | no |
| Packaged: | 2025-01-22 05:08:41 UTC; thompsre |
| Author: | Reid F. Thompson [aut, cre] |
| Maintainer: | Reid F. Thompson <[email protected]> |
| Date/Publication: | 2025-01-22 05:20:02 UTC |
| Repository: | https://reidt03.r-universe.dev |
| RemoteUrl: | https://github.com/cran/RadOnc |
| RemoteRef: | HEAD |
| RemoteSha: | a9fe57bf5f5d9fa642d52807a32b0655135a0760 |
Index of help topics:
DVH-class Class '"DVH"'
DVH.list-class Class '"DVH.list"'
LQE Linear Quadratic Extrapolated (LQE) Dose
Conversion
RTdata-class Class '"RTdata"'
RadOnc-package Analytical Tools for Radiation Oncology
calculate.DVH Calculate DVH data for one or more structure(s)
using a dose grid
compareStructures Compare Axially-Defined Three-Dimensional
Structures
gEUD Generalized Equivalent Uniform Dose (gEUD)
Calculation
get.HU Extract Hounsfield Unit (HU) data for one or
more structure(s) from a CT image
johndoe DVH data for 'John Doe' and 'Jane Doe'; 3D
structural data for 'cord', 'mandible', and
'teeth'; RT data for 'Jane Doe'; and a zDVH
object for 'stomach'
plot-methods Additional Methods for Function 'plot' in
Package 'graphics'
read.DICOM.RT Read DICOM-RT data from an input directory
read.DVH Read DVH data from input file
structure.list-class Class '"structure.list"'
structure3D-class Class '"structure3D"'
subset.DVH.list Extract a subset of a larger DVH list
zDVH-class Class '"zDVH"'
Further information is available in the following vignettes:
RadOnc |
Documentation (source, pdf) |
Reid F. Thompson [aut, cre]
Maintainer: Reid F. Thompson <[email protected]>
Thompson, R.F. (2014) RadOnc: An R Package for Analysis of Dose-Volume Histogram and Three-Dimensional Structural Data. J Radiat Oncol Inform 6(1):98-110.
DVH, DVH.list, structure3D, structure.list, RTdata
## See sub-documentation for detailed examples of important package functions #### See sub-documentation for detailed examples of important package functions ##
Function to calculate DVH data for one or more structure(s) using a dose grid.
## S4 method for signature 'RTdata,missing' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'RTdata,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'structure3D,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'structure.list,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL)## S4 method for signature 'RTdata,missing' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'RTdata,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'structure3D,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL) ## S4 method for signature 'structure.list,array' calculate.DVH(x, dose, resolution.xyz=c(0.2,0.2,NA), resolution.dose=0.01, method=NULL, dose.units=NULL)
x |
One of either a |
dose |
Object of class |
resolution.xyz |
A numeric list containing three positive values representing x, y, and z resolution to be used for DVH calculation (specified in units of mm). The smaller each value, the longer the overall calculation time (default is |
resolution.dose |
A positive numeric value specifying the dose calculation interval (bin width) for DVH calculation (values interpreted in Gy). |
method |
Character value specifying the DVH calculation algorithm to employ. Must be one of |
dose.units |
Value specifying units of dose. Must be one of |
Returns a single calculated "DVH" object or a "DVH.list" object consisting of multiple DVHs where relevant, or otherwise a "zDVH" or "DVH.list" containing multiple zDVHs when method="axial".
Reid F. Thompson ([email protected])
Straube, W., Matthews, J., Bosch, W., and Purdy, J.A. (2005) DVH Analysis: Consequences for Quality Assurance of Multi-Institutional Clinical Trials. Med Phys 32(6):2021.
data("RadOnc") # zDVHs <- calculate.DVH(janedoe.RTdata, method="axial")data("RadOnc") # zDVHs <- calculate.DVH(janedoe.RTdata, method="axial")
Three-dimensional structural comparison of a structure.list composed of two or more structure3D objects.
compareStructures(structures, method = NULL, hausdorff.method = NULL, verbose = TRUE, plot = TRUE, pixels = 100)compareStructures(structures, method = NULL, hausdorff.method = NULL, verbose = TRUE, plot = TRUE, pixels = 100)
structures |
An object of class |
method |
One of |
hausdorff.method |
One of |
verbose |
Logical value (default is |
plot |
Logical value (default is |
pixels |
Integer value (default is |
When method = "hausdorff", the function returns a NxN matrix of pairwise Hausdorff distances, where N is the number of structures in structures. When method = "axial" or method = "surface", the function returns a Mx(N+3) dimensional matrix representing a list of M points in three-dimensional space and a table of values denoting whether each point is internal or external to each structure (note that the first three columns in the matrix represent the xyz coordinates for each point and values of 1 and 0 represent internal and external points, respectively).
Reid F. Thompson ([email protected])
data("RadOnc") compareStructures(teeth, method="DSC") # teeth.compare <- compareStructures(teeth, method="axial", plot=TRUE) # compareStructures(teeth, method="hausdorff", hausdorff.method="mean")data("RadOnc") compareStructures(teeth, method="DSC") # teeth.compare <- compareStructures(teeth, method="axial", plot=TRUE) # compareStructures(teeth, method="hausdorff", hausdorff.method="mean")
"DVH"
A data structure containing Dose-Volume Histogram (DVH) data and associated parameters for a single structure
Objects can be created by calls of the form new("DVH", patient, structure.name, structure.volume, type, dose.max, dose.min, dose.mean, dose.median, dose.mode, dose.STD, conf.index, equiv.sphere, gradient, plan.sum, dose.rx, dose.fx, doses, dose.type, dose.units, volumes, volume.type, ...).
patient:Name of the patient (e.g. "Jane Doe")
ID:Additional patient identifier or medical record number (e.g. "123456789")
structure.name:Name of the structure (e.g. "Stomach")
structure.volume:Volume of the structure (in cubic centimeters)
type:A character string specifying the DVH type (must be one of "cumulative" or "differential")
dose.max:Maximum (point) dose contained within the structure
dose.min:Minimum dose contained within the structure
dose.mean:Mean dose to the structure
dose.median:Median dose to the structure
dose.mode:Modal dose to the structure
dose.STD:Standard deviation of dose to the structure
conf.index:Conformality index
equiv.sphere:Equivalent sphere (diameter in centimeters)
gradient:Dose gradient (in centimeters)
plan.sum:Logical specifying whether or not data represents a plan sum (default is FALSE)
dose.rx:Prescription dose (in units specified by dose.units)
dose.fx:Fractional dose (in units specified by dose.units)
rx.isodose:Isodose line (%) receiving prescription dose (default is 100%)
doses:List of doses corresponding to "volumes"
dose.type:A character string specifying the dose type (must be one of "relative" or "absolute")
dose.units:A character string specifying the dose units (must be one of "cGy" or "Gy")
volumes:List of volumes corresponding to "doses"
volume.type:A character string specifying the volume type (must be one of "relative" or "absolute")
Extract dose or volume parameter(s) from DVH object. Only one parameter may be specified at a time. Parameter specification should be of the form ["<A><B><C>"]: <A> is equivalent to "V" or "D", representing a volume or dose, respectively; <B> usually denotes a numerical value specifying the dose or volume; and <C> represents the dose or volume units ("cGy", "Gy", "%", or "cc"). An example would be ["V20Gy"] which represents the volume of the structure receiving at least 20Gy dose. Dose ranges may also be specified, for instance ["V10-20Gy"] or ["V<20Gy"]. Specialized dosimetric keywords may also be used: "Dmax" (maximum dose), "Dmin" (minimum dose), "Dmean" (mean dose), "Dmedian" (median dose), "Dintegral" (estimated integral dose), "DRx" (prescription dose), and "volume" (total structure volume). If an improper parameter is specified however, NA results will be returned. See package documentation (vignette) for more details.
Extract a given parameter from a DVH object
Assign a value to a given parameter within a DVH object
Combine multiple DVH objects into a single list
Plot DVH object (see link{lines})
Extract maximum dose from DVH object
Extract mean dose from DVH object
Extract minimum dose from DVH object
Extract structure name from DVH object
Assign structure name to DVH object
Plot DVH object
Plot DVH object (see link{points})
signature(x = "DVH"): Display summary of DVH object
signature(x = "DVH"): Extract dose range from DVH object
signature(x = "DVH"): Display summary of DVH object
signature(x = "DVH"): Compute the total (summed) DVH from two or more DVH objects. Note that structures are assumed to be non-overlapping; any overlaps in structure volumes may generate inaccurate dose summation.
Reid F. Thompson ([email protected])
# Description of structure/slots in class showClass("DVH")# Description of structure/slots in class showClass("DVH")
"DVH.list"
A data structure containing one or more Dose-Volume Histogram (DVH) objects
Objects can be created by calls of the form new("DVH.list", structures, ...).
structures:List of DVH objects
Extract subset of DVH list based on pattern matching with structure names (regular expressions may be specified if desired, see regex for more details). Note that case-insensitive matching is supported using the "(?i)" prefix, such that DVHs["(?i)LIVER"] will match any combination of upper and lowercase letters spelling "liver".
Extract single DVH object from DVH list
Replace single DVH object in DVH list
Replace multiple elements of DVH list
Extract dose or volume parameter(s) from DVH objects within DVH list. Note that multiple parameters may be specified by use of the comma (e.g. \$"V20Gy,D5%"). See DVH documentation ([] usage) for additional details. Note that this functionality can also be used to extract patient name(s) and/or identifier(s) (e.g. \$patients or $ID).
Convert a DVH.list object to a list containing individual DVH objects. Note that the reverse conversion can be performed using the as command and specifying class="DVH.list".
Combine two or more DVH lists and/or DVH objects
Apply function to a list of DVH objects
Extract number of DVH objects in DVH list
Compute the median absolute deviation (i.e. the median of the absolute deviations from the median) for all doses extracted from DVH object list
Compute the maximum dose contained within the DVH list
Compute the mean DVH from all DVH objects within the list
Compute the median DVH from all DVH objects within the list
Compute the minimum dose contained within the DVH list
Extract structure names for DVH objects in DVH list
Assign structure name(s) to one or more DVH objects in DVH list
Display summary of DVH list
Compute the range (minimum and maximum doses) contained within the DVH list
Return a DVH list whose DVH objects are in reverse order
Compute the standard deviation for all doses extracted from DVH object list
Display summary of DVH list
Compute the total (summed) DVH from all DVH objects within the list. Note that structures are assumed to be non-overlapping; any overlaps in structure volumes may generate inaccurate dose summation.
Apply Student's t-Test to compare two DVH lists (see also t.test)
Compute the variance for all doses extracted from DVH object list
Apply Wilcoxon Rank Sum and Signed Rank Tests to compare two DVH lists (see also wilcox.test)
Reid F. Thompson ([email protected])
# Description of structure/slots in class showClass("DVH.list") data(list="RadOnc", package="RadOnc") print(johndoe) plot(johndoe[c("LIVER", "PTV")], plot.type="i", col=c("red","blue"), lty=1:2, lwd=1:2)# Description of structure/slots in class showClass("DVH.list") data(list="RadOnc", package="RadOnc") print(johndoe) plot(johndoe[c("LIVER", "PTV")], plot.type="i", col=c("red","blue"), lty=1:2, lwd=1:2)
Function to extract Hounsfield Unit (HU) data for one or more structure(s) from a CT image.
## S4 method for signature 'RTdata,missing' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL) ## S4 method for signature 'structure3D,array' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL) ## S4 method for signature 'structure.list,array' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL)## S4 method for signature 'RTdata,missing' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL) ## S4 method for signature 'structure3D,array' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL) ## S4 method for signature 'structure.list,array' get.HU(x, CT, resolution.xyz=NA, resolution.HU=1, method=NULL)
x |
One of either a |
CT |
Object of class |
resolution.xyz |
A numeric list containing three positive values representing x, y, and z resolution to be used for Hounsfield Unit (HU) interpolation from CT imaging data (specified in units of mm). The smaller each value, the longer the overall calculation time (default is |
resolution.HU |
A positive numeric value specifying the HU calculation interval (bin width) for histogram calculation. |
method |
Character value specifying the Hounsfield Unit (HU) calculation algorithm to employ. Must be |
Returns a single calculated "histogram" object or a "list" of "histogram" objects consisting of Hounsfield Unit values contained within the input "structure3D" or "structure.list", respectively.
Reid F. Thompson ([email protected])
This function and its associated methods calculate gEUD value(s) for a given DVH or DVH.list object.
## S4 method for signature 'DVH,numeric' gEUD(x, a, dose.units = c("cGy", "Gy")) ## S4 method for signature 'DVH.list,numeric' gEUD(x, a, dose.units = c("cGy", "Gy"))## S4 method for signature 'DVH,numeric' gEUD(x, a, dose.units = c("cGy", "Gy")) ## S4 method for signature 'DVH.list,numeric' gEUD(x, a, dose.units = c("cGy", "Gy"))
x |
Can represent either an object of class |
a |
Numeric value specifying tissue-specific parameter, should be negative for target structures (e.g. tumor) and positive for organs at risk. For |
dose.units |
Value specifying dose units (must be one of |
Returns a numeric vector containing the gEUD values (in units of dose.units) for all input objects.
Reid F. Thompson ([email protected])
Thieke, C., Bortfeld, T., Niemierko, A., and Nill, S. (2003) From physical dose constraints to equivalent uniform dose constraints in inverse radiotherapy planning. Med Phys 30(9), 2332-2339.
data("RadOnc") gEUD(janedoe, 1) == unlist(janedoe$"Dmean") gEUD(janedoe, Inf) == unlist(janedoe$"Dmax") gEUD(janedoe, -Inf) == unlist(janedoe$"Dmin")data("RadOnc") gEUD(janedoe, 1) == unlist(janedoe$"Dmean") gEUD(janedoe, Inf) == unlist(janedoe$"Dmax") gEUD(janedoe, -Inf) == unlist(janedoe$"Dmin")
This function and its associated methods calculate LQE-weighted dose(s) for a given DVH or DVH.list object, allowing iso-effect conversion between one or more DVH(s) employing different dose fractionation.
## S4 method for signature 'DVH,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = c("cGy", "Gy")) ## S4 method for signature 'DVH.list,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = NULL) ## S4 method for signature 'numeric,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = c("cGy", "Gy"))## S4 method for signature 'DVH,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = c("cGy", "Gy")) ## S4 method for signature 'DVH.list,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = NULL) ## S4 method for signature 'numeric,numeric' LQE(x, aB, fractions = NULL, N = NULL, dose.units = c("cGy", "Gy"))
x |
Can represent either numeric value(s) or otherwise an object of class |
aB |
Numeric value specifying tissue-specific parameter "alpha/beta ratio". Multiple values may be specified for LQE conversion of |
fractions |
Numeric value specifying the fraction sizes in which doses are deposited. Multiple values may be specified for LQE conversion of |
N |
Numeric value specifying the number of fractions in which doses are deposited. Multiple values may be specified for LQE conversion of |
dose.units |
Value specifying output dose units (must be one of |
Returns a DVH or DVH.list object, corresponding to original input type for parameter x.
Reid F. Thompson ([email protected])
Barendsen, G.W. (1982) Dose fractionation, dose-rate and iso-effect relationships for normal-tissue response. Int J Radiat Oncol Biol Phys 8(11):1981-1997.
# 5x 300cGy == 9x 200cGy (1800cGy isoeffective dose) LQE(1500, aB=3, fractions=c(300, 200), dose.units="cGy") LQE(15, aB=3, N=c(5, 9), dose.units="Gy") LQE(18, aB=3, fractions=c(2, 3), dose.units="Gy") # Multiple simultaneous numerical queries LQE(c(4500, 5400), aB=3, fractions=c(300, 200), dose.units="cGy") # DVH processing LQE(janedoe[["LIVER"]],aB=3,fractions=200,dose.units="cGy") # DVH list processing (default dose.units is "cGy") plot(janedoe) plot(LQE(janedoe,aB=3,fractions=200),col="red",new=FALSE)# 5x 300cGy == 9x 200cGy (1800cGy isoeffective dose) LQE(1500, aB=3, fractions=c(300, 200), dose.units="cGy") LQE(15, aB=3, N=c(5, 9), dose.units="Gy") LQE(18, aB=3, fractions=c(2, 3), dose.units="Gy") # Multiple simultaneous numerical queries LQE(c(4500, 5400), aB=3, fractions=c(300, 200), dose.units="cGy") # DVH processing LQE(janedoe[["LIVER"]],aB=3,fractions=200,dose.units="cGy") # DVH list processing (default dose.units is "cGy") plot(janedoe) plot(LQE(janedoe,aB=3,fractions=200),col="red",new=FALSE)
plot in Package graphics These additional methods extend function plot in package graphics, enabling DVH visualization in package RadOnc
## S3 method for class 'DVH' plot(x, ..., plot.type = NULL) ## S3 method for class 'DVH.list' plot(x, ..., plot.type = NULL)## S3 method for class 'DVH' plot(x, ..., plot.type = NULL) ## S3 method for class 'DVH.list' plot(x, ..., plot.type = NULL)
x |
Can represent either an object of class |
... |
May contain any number of objects of class |
plot.type |
A character string specifying the type of plot to generate, must be one of |
See package vignette and examples (below) for more details about each plotting subtype.
alphaWhen plot.type="ttest", "wilcox", or "correlation", this specifies the numerical value (threshold) used to display significant p-values.
angleThe slope of shading lines, given as an angle in counter-clockwise degrees (default is 45). This parameter is ignored if density=NULL or NA or wherever fill=FALSE or is ignored (e.g. when plot.type="individual" or "bars"). Also note that this paramater can represent a list of different angles, with length of the list corresponding to the number of DVH or DVH.list objects.
backA character value specifying the back-facing surface fill method when x is a zDVH object (the parameter is otherwise ignored). Value must be one of "filled", "lines", "points", or "culled". Default value is assigned from input parameter front.
centerA character value specifying where to plot the center of a group when plot.type="grouped" (the parameter is otherwise ignored). Value must be one of "mean" or "median".
Note: As of package v.1.0.3, this parameter is considered defunct and will be disregarded accordingly.
colThe color to be used for drawing lines. This parameter can also represent a list of different colors, with length corresponding to the number of DVH, zDVH, or DVH.list objects (if plot.type="individual", number of colors should correspond to number of individual DVH objects).
When plot.type="bars", col instead represents a list of colors used to define the shading scheme applied to the entire dose range. Default color scheme is a standard rainbow, with colors ranging from "blue" to "red". Actual default is specified as rev(rainbow(n=10, start=0, end=2/3)). See colors for more options and information.
densityThe density of shading lines, in lines per inch. The default value of NULL means that no shading lines are drawn. A zero value of density means no shading nor filling, whereas negative values and NA suppress shading lines but allow solid color filling. Note that this paramater can also represent a list of different densities, with length of the list corresponding to the number of DVH or DVH.list objects.
fillLogical, defaulting to TRUE. Determines whether or not to draw shading around groups of DVH lines. Note that this parameter is relevant when plot.type="grouped", "ttest" or "wilcox" (it is ignored when plot.type="individual" or "bars").
fill.ltyThe line type used for shading (per density and angle parameters). See lty above for further specifications of line types. Note that this paramater can represent a list of different line types, with length corresponding to the number of DVH or DVH.list objects.
fill.transparencyFactor modifying the transparency of filling/shading (value must be between [0,1]), with fill.transparency=0 specifying complete transparency and 1 specifying complete opacity. Note that this parameter can represent a list of different transparency factors, with length corresponding to the number of DVH or DVH.list objects. Default value is line.transparency/2.
frontA character value specifying the front-facing surface fill method when x is a zDVH object (the parameter is otherwise ignored). Value must be one of "filled" (default), "lines", "points", or "culled".
gridLogical, defaulting to FALSE. Determines whether or not to draw gridlines on 2D plot. Note that this parameter is relevant when plot.type="individual", "grouped", "ttest", or "wilcox" (it is ignored when plot.type="bars" or when plotting zDVH objects).
highlightThe color to be used for shading p-value data when plot.type="ttest" or "wilcox". See colors for more options and information.
legendValue specifying the location to draw a figure legend, must be one of "topright", "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "right", or "center". These keywords place the legend on the inside of the plot frame at the location specified. Partial argument matching is used. If legend=NA (default), the legend is not drawn.
When plot.type="bars", legend is interpreted instead as a logical value and must be either TRUE (default) or FALSE. If TRUE, labels are drawn at the bottom of the plot, outside of the actual plotting frame.
Note that legend parameter is ignored when plot.type="wilcox" and panel.lower="difference".
legend.labelsA character or expression vector specifying the text to appear in the legend, when relevant. Length of legend.labels must match the numer of DVH and DVH.list objects, otherwise legend text will default to the form: "Group 1", "Group 2", ...
line.transparencyFactor modifying the transparency of line drawings (value must be between [0,1]), with fill.transparency=0 specifying complete transparency and 1 (default) specifying complete opacity. Note that this parameter can represent a list of different transparency factors, with length corresponding to the number of DVH or DVH.list objects (if plot.type="individual", number of transparency factors should correspond to number of individual DVH objects).
ltyThe line type. Line types can either be specified as an integer (0=blank, 1=solid (default), 2=dashed, 3=dotted, 4=dotdash, 5=longdash, 6=twodash) or as one of the character strings "blank", "solid", "dashed", "dotted", "dotdash", "longdash", or "twodash", where "blank" uses 'invisible lines' (i.e., does not draw them).
Alternatively, a string of up to 8 characters (from c(1:9, "A":"F")) may be given, giving the length of line segments which are alternatively drawn and skipped (see par for more details). Note that this paramater can also represent a list of different line types, with length corresponding to the number of DVH or DVH.list objects (if plot.type="individual", number of line types should correspond to number of individual DVH objects).
lwdThe line width, a positive number, defaulting to 1. The interpretation is device-specific, and some devices do not implement line widths less than one (see the help on the device for details of the interpretation). Note that this paramater can also represent a list of different line widths, with length of the list corresponding to the number of DVH or DVH.list objects (if plot.type="individual", number of line widths should correspond to number of individual DVH objects).
mainAn overall title for the plot (see title, default is "").
multiplierA single numerical value (default is 1) specifying the degree to which group display width should be shrunken or magnified. This parameter is only processed when plot.type="grouped" or "ttest" and width="mad", "sd", or "var".
newLogical, defaulting to TRUE. If set to FALSE, the next high-level plotting command (actually plot.new) should not clean the frame before drawing as if it were on a new device. It is an error (ignored with a warning) to try to use new=FALSE on a device that does not currently contain a high-level plot.
panel.lowerValue specifying the lower panel plot content when plot.type="wilcox" (panel.lower must be one of "grouped" or "wilcox" [default]). Partial argument matching is used.
When panel.lower="wilcox", the median groupwise differences will be displayed with associated confidence intervals obtained from wilcox.test(). When panel.lower="grouped", the individual groups are displayed with surrounding user-specified intervals (see width, quantile, and multiplier parameters).
quantileA numeric vector containing two values in [0,1] (default is the interquartile range: (0.25, 0.75)), specifying the lower and upper probabilities (respectively) to be used when width="quantile" and plot.type="grouped" or "ttest". See quantile for more details.
widthA character vector specifying the width of shading to use, when relevant (for a group of DVHs). Value must be one of "range" (default), "mad", "IQR", "quantile", "var", or "sd", specifying the absolute range, the mean-absolute-deviation, the interquartile (25-75%) range, the arbitrary inter-quantile range (see quantile parameter), the group variance, or standard deviation, respectively. This parameter is ignored unless plot.type="grouped". If plot.type="ttest", the parameter can be optionally specified (if width=NULL (default), shading will default to the confidence interval).
xlimA numeric vector of length 2 specifying the minimum and maximum x coordinates for plotting (note that this parameter is ignored when plot.type="bars", new=FALSE, or plotting object(s) of class zDVH).
ylimA numeric vector of length 2 specifying the minimum and maximum y coordinates for plotting (note that this parameter is ignored when plot.type="bars", new=FALSE, or plotting object(s) of class zDVH).
alternativeWhen plot.type="ttest", "wilcox", or "correlation", alternative indicates the alternative hypothesis and must be one of "two.sided", "greater" or "less". You can specify just the initial letter. "greater" corresponds to positive association, "less" to negative association. See cor.test for more details.
doseValue specifying dose scale (must be one of "relative" or "absolute").
dose.unitsValue specifying dose units (must be one of "cGy" or "Gy").
exactWhen plot.type="wilcox" or plot.type="correlation" and method="kendall" or "spearman", exact specifies a logical indicating whether an exact p-value should be computed. See cor.test or wilcox.test for more details.
methodWhen plot.type="correlation", method specifies a character string indicating which correlation coefficient is to be computed. Value must be one of "pearson" (default), "kendall", or "spearman". See cor.test for more details.
muWhen plot.type="ttest" or "wilcox", specifies an optional parameter used to form the null hypothesis. See t.test or wilcox.test for more details.
pairedA logical value (default is FALSE) specifying whether or not to perform paired groupwise comparisons when plot.type="ttest" or "wilcox".
typeValue specifying type of dose-volume histogram to plot (must be one of "cumulative" or "differential").
volumeValue specifying volume scale (must be one of "relative" or "absolute").
# plot(x, ..., plot.type="individual") OARs <- c("LIVER","STOMACH","DUODENUM") cols <- c("red", "darkgreen", "blue") plot(johndoe[OARs], col=cols, lty=1:3, legend="topright", legend.labels=OARs, main="OARs") # plot(x, ..., plot.type="bars") plot(janedoe[2:9], plot.type="bars", volume="absolute",dose="relative") # plot(x, ..., plot.type="grouped") plot(c(johndoe["STOMACH"],janedoe["STOMACH"]), #group 1 c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 2 c(janedoe["LIVER"],johndoe["LIVER"]), #group 3 c(johndoe["DUODENUM"],janedoe["DUODENUM"]), #group 4 plot.type="grouped", col=c("orange","green","blue","red"), lwd=2, dose="relative") # plot(x, ..., plot.type="ttest") # OARs <- c("LIVER", "STOMACH", "SMALL_BOWEL") # plot(c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 1 # c(janedoe[OARs],johndoe[OARs]), #group 2 # plot.type="t", col=c("red", "blue"), lty=2, fill.lty=1, main="Target v. OAR t-Test") # plot(x, ..., plot.type="wilcox") # plot(c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 1 # c(janedoe[OARs],johndoe[OARs]), #group 2 # plot.type="w", col=c("red", "blue"), lty=2, fill.lty=1, main="Target v. OAR", # panel.lower="grouped") # plot(x, ..., plot.type="correlation") # plot(janedoe, sample(1:100, 10), plot.type="correlation", method="kendall")# plot(x, ..., plot.type="individual") OARs <- c("LIVER","STOMACH","DUODENUM") cols <- c("red", "darkgreen", "blue") plot(johndoe[OARs], col=cols, lty=1:3, legend="topright", legend.labels=OARs, main="OARs") # plot(x, ..., plot.type="bars") plot(janedoe[2:9], plot.type="bars", volume="absolute",dose="relative") # plot(x, ..., plot.type="grouped") plot(c(johndoe["STOMACH"],janedoe["STOMACH"]), #group 1 c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 2 c(janedoe["LIVER"],johndoe["LIVER"]), #group 3 c(johndoe["DUODENUM"],janedoe["DUODENUM"]), #group 4 plot.type="grouped", col=c("orange","green","blue","red"), lwd=2, dose="relative") # plot(x, ..., plot.type="ttest") # OARs <- c("LIVER", "STOMACH", "SMALL_BOWEL") # plot(c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 1 # c(janedoe[OARs],johndoe[OARs]), #group 2 # plot.type="t", col=c("red", "blue"), lty=2, fill.lty=1, main="Target v. OAR t-Test") # plot(x, ..., plot.type="wilcox") # plot(c(johndoe[c("CTV","PTV")],janedoe[c("CTV","PTV")]), #group 1 # c(janedoe[OARs],johndoe[OARs]), #group 2 # plot.type="w", col=c("red", "blue"), lty=2, fill.lty=1, main="Target v. OAR", # panel.lower="grouped") # plot(x, ..., plot.type="correlation") # plot(janedoe, sample(1:100, 10), plot.type="correlation", method="kendall")
List of 10 DVH objects corresponding to structures (e.g. liver) for patients 'John Doe' and 'Jane Doe'; Two structure3D objects ('cord' and 'mandible') and one structure list ('teeth') containing 3 structures; an RTdata object for 'Jane Doe' containing dose grid information and a structure list with 3 structures; and one zDVH object ('stomach').
data(package="RadOnc")data(package="RadOnc")
The format for johndoe is:
Formal class 'DVH.list' [package "RadOnc"] with 1 slots ..@ structures:List of 10 .. ..$ LIVER :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "LIVER" .. .. .. ..@ structure.volume: num 1367 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 92.9 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 4.9 .. .. .. ..@ dose.median : num 0 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 10.8 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 1367 414 392 378 368 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ SMALL_BOWEL :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "SMALL_BOWEL" .. .. .. ..@ structure.volume: num 206 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 99.8 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 4.3 .. .. .. ..@ dose.median : num 0 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 15.3 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 206.2 43.1 39.5 37.4 35.8 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ DUODENUM :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "DUODENUM" .. .. .. ..@ structure.volume: num 93.1 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 102 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 70.7 .. .. .. ..@ dose.median : num 81.3 .. .. .. ..@ dose.mode : num 100 .. .. .. ..@ dose.STD : num 30.3 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 93.1 93.1 93 93 92.9 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ STOMACH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "STOMACH" .. .. .. ..@ structure.volume: num 304 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 101 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 7.9 .. .. .. ..@ dose.median : num 0 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 22.8 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 303.6 78 71.5 67.8 65.1 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ CTV :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "CTV" .. .. .. ..@ structure.volume: num 88.4 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 103 .. .. .. ..@ dose.min : num 96.8 .. .. .. ..@ dose.mean : num 100 .. .. .. ..@ dose.median : num 100 .. .. .. ..@ dose.mode : num 100 .. .. .. ..@ dose.STD : num 0.7 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 88.4 88.4 88.4 88.4 88.4 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ PTV :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "PTV" .. .. .. ..@ structure.volume: num 156 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 103 .. .. .. ..@ dose.min : num 84.1 .. .. .. ..@ dose.mean : num 99.6 .. .. .. ..@ dose.median : num 99.8 .. .. .. ..@ dose.mode : num 99.9 .. .. .. ..@ dose.STD : num 1.2 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 156 156 156 156 156 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ BODY :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "BODY" .. .. .. ..@ structure.volume: num 17666 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 103 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 5.6 .. .. .. ..@ dose.median : num 0 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 17.1 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 17666 3424 3290 3206 3143 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ LEFT_KIDNEY :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "LEFT_KIDNEY" .. .. .. ..@ structure.volume: num 154 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 44.4 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 4.7 .. .. .. ..@ dose.median : num 0 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 9.5 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 154.2 48.3 46.4 45.3 44.4 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ RIGHT_KIDNEY:Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "RIGHT_KIDNEY" .. .. .. ..@ structure.volume: num 155 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 98.5 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 24.2 .. .. .. ..@ dose.median : num 24.3 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 22.8 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 155 134 132 130 129 ... .. .. .. ..@ volume.type : chr "absolute" .. ..$ CORD :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "John Doe" .. .. .. ..@ ID : chr "5555555555" .. .. .. ..@ structure.name : chr "CORD" .. .. .. ..@ structure.volume: num 40.7 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 55.5 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 20.7 .. .. .. ..@ dose.median : num 4.1 .. .. .. ..@ dose.mode : num 0 .. .. .. ..@ dose.STD : num 23.2 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1026] 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 ... .. .. .. ..@ dose.type : chr "relative" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1026] 40.7 23 22.7 22.4 22.2 ... .. .. .. ..@ volume.type : chr "absolute"
The format for janedoe is:
Formal class 'DVH.list' [package "RadOnc"] with 1 slots ..@ structures:List of 10 .. ..$ LIVER :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "LIVER" .. .. .. ..@ structure.volume: num 1636 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5634 .. .. .. ..@ dose.min : num 42.7 .. .. .. ..@ dose.mean : num 707 .. .. .. ..@ dose.median : num 276 .. .. .. ..@ dose.mode : num 99.5 .. .. .. ..@ dose.STD : num 917 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ LEFT_KIDNEY :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "LEFT_KIDNEY" .. .. .. ..@ structure.volume: num 196 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 3847 .. .. .. ..@ dose.min : num 75.8 .. .. .. ..@ dose.mean : num 1021 .. .. .. ..@ dose.median : num 703 .. .. .. ..@ dose.mode : num 119 .. .. .. ..@ dose.STD : num 802 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ STOMACH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "STOMACH" .. .. .. ..@ structure.volume: num 695 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5353 .. .. .. ..@ dose.min : num 59 .. .. .. ..@ dose.mean : num 1280 .. .. .. ..@ dose.median : num 1302 .. .. .. ..@ dose.mode : num 111 .. .. .. ..@ dose.STD : num 1062 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ DUODENUM :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "DUODENUM" .. .. .. ..@ structure.volume: num 34.2 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5620 .. .. .. ..@ dose.min : num 2708 .. .. .. ..@ dose.mean : num 4755 .. .. .. ..@ dose.median : num 4943 .. .. .. ..@ dose.mode : num 5365 .. .. .. ..@ dose.STD : num 635 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ RIGHT_KIDNEY:Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "RIGHT_KIDNEY" .. .. .. ..@ structure.volume: num 224 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 4202 .. .. .. ..@ dose.min : num 102 .. .. .. ..@ dose.mean : num 1511 .. .. .. ..@ dose.median : num 1624 .. .. .. ..@ dose.mode : num 1638 .. .. .. ..@ dose.STD : num 714 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ CTV :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "CTV" .. .. .. ..@ structure.volume: num 147 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5647 .. .. .. ..@ dose.min : num 5169 .. .. .. ..@ dose.mean : num 5500 .. .. .. ..@ dose.median : num 5505 .. .. .. ..@ dose.mode : num 5500 .. .. .. ..@ dose.STD : num 59.8 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ PTV :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "PTV" .. .. .. ..@ structure.volume: num 239 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5665 .. .. .. ..@ dose.min : num 4750 .. .. .. ..@ dose.mean : num 5471 .. .. .. ..@ dose.median : num 5493 .. .. .. ..@ dose.mode : num 5500 .. .. .. ..@ dose.STD : num 98.6 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ SMALL_BOWEL :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "SMALL_BOWEL" .. .. .. ..@ structure.volume: num 232 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 4934 .. .. .. ..@ dose.min : num 59.6 .. .. .. ..@ dose.mean : num 294 .. .. .. ..@ dose.median : num 171 .. .. .. ..@ dose.mode : num 127 .. .. .. ..@ dose.STD : num 391 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 100 100 100 100 100 100 100 100 100 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ CORD :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "CORD" .. .. .. ..@ structure.volume: num 64.9 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 3443 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 732 .. .. .. ..@ dose.median : num 136 .. .. .. ..@ dose.mode : num 6.9 .. .. .. ..@ dose.STD : num 953 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 98.5 95.9 93.8 90.8 ... .. .. .. ..@ volume.type : chr "relative" .. ..$ BODY :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. ..@ patient : chr "Jane Doe" .. .. .. ..@ ID : chr "1111111111" .. .. .. ..@ structure.name : chr "BODY" .. .. .. ..@ structure.volume: num 25508 .. .. .. ..@ type : chr "cumulative" .. .. .. ..@ dose.max : num 5665 .. .. .. ..@ dose.min : num 0 .. .. .. ..@ dose.mean : num 478 .. .. .. ..@ dose.median : num 66.4 .. .. .. ..@ dose.mode : num 0.4 .. .. .. ..@ dose.STD : num 946 .. .. .. ..@ conf.index : num 0 .. .. .. ..@ equiv.sphere : num 0 .. .. .. ..@ gradient : num 0 .. .. .. ..@ plan.sum : log FALSE .. .. .. ..@ dose.rx : num 5500 .. .. .. ..@ dose.fx : num 25 .. .. .. ..@ rx.isodose : num 100 .. .. .. ..@ doses : num [1:1133] 0 5 10 15 20 25 30 35 40 45 ... .. .. .. ..@ dose.type : chr "absolute" .. .. .. ..@ dose.units : chr "cGy" .. .. .. ..@ volumes : num [1:1133] 100 77.7 75.1 73 71.3 ... .. .. .. ..@ volume.type : chr "relative"
The format for janedoe.RTdata is:
Formal class 'RTdata' [package "RadOnc"] with 4 slots ..@ name : chr "Jane Doe" ..@ CT : logi[0 , 0 , 0 ] ..@ dose : num [1:74, 1:72, 1:51] 2.79 2.87 2.96 3.08 3.32 ... .. ..- attr(*, "dimnames")=List of 3 .. .. ..$ : chr [1:74] "-57.5120192" "-55.0120192" "-52.5120192" "-50.0120192" ... .. .. ..$ : chr [1:72] "-309.3547858" "-306.8547858" "-304.3547858" "-301.8547858" ... .. .. ..$ : chr [1:51] "-102" "-99" "-96" "-93" ... ..@ structures:Formal class 'structure.list' [package "RadOnc"] with 1 slots .. .. ..@ structures:List of 3 .. .. .. ..$ STOMACH:Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. .. .. ..@ name : chr "STOMACH" .. .. .. .. .. ..@ volume : num 0 .. .. .. .. .. ..@ volume.units : chr "cc" .. .. .. .. .. ..@ coordinate.units: chr "cm" .. .. .. .. .. ..@ vertices : num [1:9222, 1:3] -23.4 -21.5 -19.5 -17.6 -15.6 ... .. .. .. .. .. ..@ origin : num [1:3] 42.5 -202.6 -26.8 .. .. .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. .. .. ..@ closed.polys :List of 52 .. .. .. .. .. .. ..$ : num [1:192, 1:3] -23.4 -21.5 -19.5 -17.6 -15.6 ... .. .. .. .. .. .. ..$ : num [1:188, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 7.81 ... .. .. .. .. .. .. ..$ : num [1:4, 1:3] 70.3 70.1 70.3 70.5 -191.9 ... .. .. .. .. .. .. ..$ : num [1:192, 1:3] -5.86 -3.91 -1.95 0 1.95 ... .. .. .. .. .. .. ..$ : num [1:182, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:180, 1:3] -35.2 -33.2 -31.2 -29.3 -27.3 ... .. .. .. .. .. .. ..$ : num [1:174, 1:3] -35.2 -33.2 -31.2 -29.3 -27.3 ... .. .. .. .. .. .. ..$ : num [1:180, 1:3] -33.2 -31.2 -29.3 -27.3 -25.4 ... .. .. .. .. .. .. ..$ : num [1:170, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:168, 1:3] -3.91 -1.95 0 1.95 3.91 ... .. .. .. .. .. .. ..$ : num [1:160, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:152, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:174, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 6.48 ... .. .. .. .. .. .. ..$ : num [1:176, 1:3] -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 7.81 9.77 ... .. .. .. .. .. .. ..$ : num [1:176, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:4, 1:3] 7.81 6.99 7.81 8.11 -158.68 ... .. .. .. .. .. .. ..$ : num [1:194, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:4, 1:3] -29.3 -29.3 -29.3 -29.3 -160.8 ... .. .. .. .. .. .. ..$ : num [1:194, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 7.81 ... .. .. .. .. .. .. ..$ : num [1:192, 1:3] -13.67 -11.72 -9.77 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:214, 1:3] -11.72 -9.77 -7.81 -5.86 -3.91 ... .. .. .. .. .. .. ..$ : num [1:216, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 4.51 5.86 ... .. .. .. .. .. .. ..$ : num [1:214, 1:3] -11.72 -9.77 -7.81 -5.86 -3.91 ... .. .. .. .. .. .. ..$ : num [1:204, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:208, 1:3] -5.86 -3.91 -1.95 0 1.95 3.81 3.91 5.86 7.81 9.77 ... .. .. .. .. .. .. ..$ : num [1:210, 1:3] 7.81 9.77 11.72 13.67 15.63 ... .. .. .. .. .. .. ..$ : num [1:4, 1:3] 7.81 7.71 7.81 7.91 -164.59 ... .. .. .. .. .. .. ..$ : num [1:208, 1:3] -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 7.81 9.77 ... .. .. .. .. .. .. ..$ : num [1:198, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 0 1.95 3.91 5.86 7.81 ... .. .. .. .. .. .. ..$ : num [1:198, 1:3] -1.95 0 1.95 3.91 5.57 ... .. .. .. .. .. .. ..$ : num [1:232, 1:3] 1.95 3.91 5.86 6.47 7.81 ... .. .. .. .. .. .. ..$ : num [1:236, 1:3] 7.81 9.77 11.72 13.67 15.63 ... .. .. .. .. .. .. ..$ : num [1:290, 1:3] 1.95 3.91 5.86 7.81 9.77 ... .. .. .. .. .. .. ..$ : num [1:278, 1:3] 21.5 23.4 25.4 27.3 28.5 ... .. .. .. .. .. .. ..$ : num [1:246, 1:3] 44.9 46.9 48.8 50.8 52.7 ... .. .. .. .. .. .. ..$ : num [1:248, 1:3] 44.9 46.9 48.8 50.8 52.7 ... .. .. .. .. .. .. ..$ : num [1:234, 1:3] 56.6 58.6 60.5 62.5 64.5 ... .. .. .. .. .. .. ..$ : num [1:234, 1:3] 62.5 64.5 66.4 68.4 70.3 ... .. .. .. .. .. .. ..$ : num [1:232, 1:3] 70.3 72.3 74.2 76.2 78.1 ... .. .. .. .. .. .. ..$ : num [1:216, 1:3] 78.1 80.1 82 84 85.9 ... .. .. .. .. .. .. ..$ : num [1:212, 1:3] 80.1 82 84 85.9 87.9 ... .. .. .. .. .. .. ..$ : num [1:202, 1:3] 80.1 82 84 85.9 86.4 ... .. .. .. .. .. .. ..$ : num [1:198, 1:3] 80.1 82 84 85.9 87.9 ... .. .. .. .. .. .. ..$ : num [1:180, 1:3] 87.9 89.5 89.8 91.8 93.8 ... .. .. .. .. .. .. ..$ : num [1:176, 1:3] 91.8 93.8 95.7 97.7 99.6 ... .. .. .. .. .. .. ..$ : num [1:158, 1:3] 84 85.9 87.9 89.8 90 ... .. .. .. .. .. .. ..$ : num [1:158, 1:3] 84 85.9 87.9 88.1 89.8 ... .. .. .. .. .. .. ..$ : num [1:142, 1:3] 80.1 82 84 85.9 87.9 ... .. .. .. .. .. .. ..$ : num [1:146, 1:3] 78.1 80.1 82 84 85.9 ... .. .. .. .. .. .. ..$ : num [1:130, 1:3] 76.2 78.1 80.1 82 84 ... .. .. .. .. .. .. ..$ : num [1:74, 1:3] 80.1 82 84 85.9 86.1 ... .. .. .. .. .. .. ..$ : num [1:70, 1:3] 82 84 85.9 87.3 87.9 ... .. .. .. .. .. .. ..- attr(*, "dim")= int [1:2] 52 1 .. .. .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 22 slots .. .. .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. .. .. ..@ structure.name : chr "STOMACH" .. .. .. .. .. .. .. ..@ structure.volume: num 699 .. .. .. .. .. .. .. ..@ type : chr "differential" .. .. .. .. .. .. .. ..@ dose.max : num 53.6 .. .. .. .. .. .. .. ..@ dose.min : num 0.594 .. .. .. .. .. .. .. ..@ dose.mean : num 12.8 .. .. .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. .. .. ..@ dose.rx : num 55 .. .. .. .. .. .. .. ..@ dose.fx : num 25 .. .. .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. .. .. ..@ doses : num [1:5665] 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 ... .. .. .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. .. .. ..@ dose.units : chr "Gy" .. .. .. .. .. .. .. ..@ volumes : num [1:5665] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. .. .. .. ..@ volume.type : chr "absolute" .. .. .. ..$ CTV :Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. .. .. ..@ name : chr "CTV" .. .. .. .. .. ..@ volume : num 0 .. .. .. .. .. ..@ volume.units : chr "cc" .. .. .. .. .. ..@ coordinate.units: chr "cm" .. .. .. .. .. ..@ vertices : num [1:2440, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. ..@ origin : num [1:3] -11.9 -237.5 -52.7 .. .. .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. .. .. ..@ closed.polys :List of 23 .. .. .. .. .. .. ..$ : num [1:56, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:74, 1:3] -31.2 -29.3 -27.3 -25.4 -23.4 ... .. .. .. .. .. .. ..$ : num [1:92, 1:3] -27.3 -25.4 -23.4 -21.5 -19.5 ... .. .. .. .. .. .. ..$ : num [1:96, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:102, 1:3] -27.3 -25.4 -23.4 -21.5 -19.5 ... .. .. .. .. .. .. ..$ : num [1:112, 1:3] -23.4 -22.5 -21.5 -19.5 -17.6 ... .. .. .. .. .. .. ..$ : num [1:116, 1:3] -39.1 -37.1 -35.2 -33.2 -31.2 ... .. .. .. .. .. .. ..$ : num [1:112, 1:3] -35.2 -33.2 -31.2 -29.3 -27.3 ... .. .. .. .. .. .. ..$ : num [1:114, 1:3] -21.5 -19.5 -17.6 -15.6 -13.7 ... .. .. .. .. .. .. ..$ : num [1:110, 1:3] -21.5 -19.5 -17.6 -15.6 -13.7 ... .. .. .. .. .. .. ..$ : num [1:112, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:108, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:116, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:120, 1:3] -11.72 -9.77 -8.79 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:126, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:124, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:124, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:120, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:110, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:106, 1:3] -13.67 -11.72 -9.77 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:102, 1:3] -13.67 -11.72 -9.77 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:100, 1:3] -11.72 -9.77 -7.81 -5.86 -3.91 ... .. .. .. .. .. .. ..$ : num [1:88, 1:3] -11.72 -9.77 -7.81 -5.86 -3.91 ... .. .. .. .. .. .. ..- attr(*, "dim")= int [1:2] 23 1 .. .. .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 22 slots .. .. .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. .. .. ..@ structure.name : chr "CTV" .. .. .. .. .. .. .. ..@ structure.volume: num 148 .. .. .. .. .. .. .. ..@ type : chr "differential" .. .. .. .. .. .. .. ..@ dose.max : num 56.5 .. .. .. .. .. .. .. ..@ dose.min : num 51.7 .. .. .. .. .. .. .. ..@ dose.mean : num 55 .. .. .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. .. .. ..@ dose.rx : num 55 .. .. .. .. .. .. .. ..@ dose.fx : num 25 .. .. .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. .. .. ..@ doses : num [1:5665] 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 ... .. .. .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. .. .. ..@ dose.units : chr "Gy" .. .. .. .. .. .. .. ..@ volumes : num [1:5665] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. .. .. .. ..@ volume.type : chr "absolute" .. .. .. ..$ PTV :Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. .. .. ..@ name : chr "PTV" .. .. .. .. .. ..@ volume : num 0 .. .. .. .. .. ..@ volume.units : chr "cc" .. .. .. .. .. ..@ coordinate.units: chr "cm" .. .. .. .. .. ..@ vertices : num [1:3314, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. ..@ origin : num [1:3] -11.8 -237.1 -52.7 .. .. .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. .. .. ..@ closed.polys :List of 27 .. .. .. .. .. .. ..$ : num [1:64, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:78, 1:3] -31.2 -29.3 -27.3 -25.4 -23.4 ... .. .. .. .. .. .. ..$ : num [1:94, 1:3] -33.2 -31.2 -29.3 -27.3 -25.4 ... .. .. .. .. .. .. ..$ : num [1:106, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:112, 1:3] -31.2 -29.3 -27.3 -25.4 -23.4 ... .. .. .. .. .. .. ..$ : num [1:126, 1:3] -33.2 -31.2 -29.3 -27.3 -25.4 ... .. .. .. .. .. .. ..$ : num [1:130, 1:3] -31.2 -29.3 -27.3 -25.4 -23.4 ... .. .. .. .. .. .. ..$ : num [1:136, 1:3] -29.3 -27.3 -25.4 -23.4 -21.5 ... .. .. .. .. .. .. ..$ : num [1:134, 1:3] -27.3 -25.4 -23.4 -21.5 -20.4 ... .. .. .. .. .. .. ..$ : num [1:136, 1:3] -41 -39.1 -37.1 -35.2 -33.2 ... .. .. .. .. .. .. ..$ : num [1:134, 1:3] -37.1 -35.2 -33.2 -31.2 -29.3 ... .. .. .. .. .. .. ..$ : num [1:132, 1:3] -23.4 -21.5 -19.5 -17.6 -15.6 ... .. .. .. .. .. .. ..$ : num [1:128, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:134, 1:3] -21.5 -19.5 -17.6 -15.6 -13.7 ... .. .. .. .. .. .. ..$ : num [1:138, 1:3] -13.67 -11.72 -9.77 -7.81 -6.71 ... .. .. .. .. .. .. ..$ : num [1:144, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:142, 1:3] -21.5 -19.5 -17.6 -15.6 -13.7 ... .. .. .. .. .. .. ..$ : num [1:144, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:142, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:140, 1:3] -21.5 -19.5 -17.6 -15.6 -13.7 ... .. .. .. .. .. .. ..$ : num [1:136, 1:3] -19.5 -17.6 -15.6 -13.7 -11.7 ... .. .. .. .. .. .. ..$ : num [1:130, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:122, 1:3] -17.58 -15.63 -13.67 -11.72 -9.77 ... .. .. .. .. .. .. ..$ : num [1:118, 1:3] -15.63 -13.67 -11.72 -9.77 -7.81 ... .. .. .. .. .. .. ..$ : num [1:116, 1:3] -13.67 -11.72 -9.77 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:104, 1:3] -13.67 -11.72 -9.77 -7.81 -5.86 ... .. .. .. .. .. .. ..$ : num [1:94, 1:3] -9.77 -7.81 -5.86 -3.91 -1.95 -0.6 0 1.95 3.91 5.14 ... .. .. .. .. .. .. ..- attr(*, "dim")= int [1:2] 27 1 .. .. .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 22 slots .. .. .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. .. .. ..@ structure.name : chr "PTV" .. .. .. .. .. .. .. ..@ structure.volume: num 241 .. .. .. .. .. .. .. ..@ type : chr "differential" .. .. .. .. .. .. .. ..@ dose.max : num 56.6 .. .. .. .. .. .. .. ..@ dose.min : num 47.1 .. .. .. .. .. .. .. ..@ dose.mean : num 54.7 .. .. .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. .. .. ..@ dose.rx : num 55 .. .. .. .. .. .. .. ..@ dose.fx : num 25 .. .. .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. .. .. ..@ doses : num [1:5665] 0 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 ... .. .. .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. .. .. ..@ dose.units : chr "Gy" .. .. .. .. .. .. .. ..@ volumes : num [1:5665] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. .. .. .. ..@ volume.type : chr "absolute"
The format for cord is:
Formal class 'structure3D' [package "RadOnc"] with 9 slots ..@ name : chr "Spinal Cord" ..@ volume : num 0 ..@ volume.units : chr "cc" ..@ coordinate.units: chr "cm" ..@ vertices : num [1:2682, 1:3] -10.74 -8.79 -6.84 -4.88 -3.13 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:2682] "" "" "" "" ... .. .. ..$ : NULL ..@ origin : num [1:3] -3.43 -235.27 -173.95 ..@ triangles : num [1:3, 1:5360] 20 1 21 1 2 22 2 3 23 3 ... ..@ closed.polys :List of 130 .. ..$ : num [1:20, 1:3] -10.74 -8.79 -6.84 -4.88 -3.13 ... .. ..$ : num [1:18, 1:3] -10.74 -8.79 -6.84 -4.88 -3.15 ... .. ..$ : num [1:20, 1:3] -6.84 -6.1 -4.88 -2.93 -2.62 -1.68 -1.77 -2.53 -2.93 -4.88 ... .. ..$ : num [1:20, 1:3] -6.84 -4.95 -4.88 -2.93 -2.16 -1.36 -1.41 -2.33 -2.93 -4.88 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -3.34 -2.93 -2.07 -1.72 -2.38 -2.93 -4.26 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -4.67 -2.93 -2.67 -2.12 -2.31 -2.93 -3.45 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -3.99 -2.93 -2.14 -1.77 -2.01 -2.93 -3.61 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -2.93 -2.91 -1.75 -1.55 -2.01 -2.93 -3.65 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -2.93 -2.62 -1.53 -1.4 -1.95 -2.93 -4.08 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -2.93 -2.51 -1.4 -1.37 -2.18 -2.93 -4.88 ... .. ..$ : num [1:18, 1:3] -8.79 -6.84 -4.88 -2.93 -1.77 -1.28 -1.89 -2.93 -3.54 -4.88 ... .. ..$ : num [1:16, 1:3] -6.84 -4.88 -2.99 -2.93 -1.06 -1.34 -2.51 -2.93 -4.88 -6.84 ... .. ..$ : num [1:18, 1:3] -6.84 -4.88 -2.93 -2.21 -0.98 -0.67 -0.8 -0.98 -2.01 -2.93 ... .. ..$ : num [1:18, 1:3] -8.79 -6.84 -4.88 -2.93 -1.37 -0.98 -0.54 -0.56 -0.98 -1.49 ... .. ..$ : num [1:20, 1:3] -8.79 -6.84 -4.88 -2.93 -1.43 -0.98 -0.34 -0.38 -0.98 -1.61 ... .. ..$ : num [1:18, 1:3] -8.79 -6.84 -4.88 -2.93 -1.36 -0.98 -0.55 -0.56 -0.98 -1.49 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -2.87 -1.03 -0.98 -0.23 -0.46 -0.98 -1.89 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -2.26 -0.98 -0.64 -0.23 -0.55 -0.98 -2.03 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -2.34 -0.98 -0.57 -0.18 -0.57 -0.98 -2.44 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -2.26 -0.98 -0.67 -0.27 -0.92 -0.98 -2.93 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -2.18 -0.98 -0.79 -0.49 -0.98 -1.12 -2.93 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -3.66 -2.93 -1.04 -0.98 -0.18 -0.16 -0.98 -1.46 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -1.51 -0.98 -0.06 0.28 -0.14 -0.98 -1.75 ... .. ..$ : num [1:18, 1:3] -6.84 -4.88 -2.93 -0.98 -0.92 0.31 0.18 -0.92 -0.98 -2.93 ... .. ..$ : num [1:18, 1:3] -6.84 -4.88 -2.93 -0.98 -0.46 0.44 -0.09 -0.98 -2.93 -4.83 ... .. ..$ : num [1:18, 1:3] -6.84 -4.88 -2.93 -0.98 -0.92 0.34 0.31 -0.98 -1.95 -2.93 ... .. ..$ : num [1:18, 1:3] -6.84 -4.88 -2.93 -1.64 -0.98 0.07 0.56 -0.69 -0.98 -2.93 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -2.83 -0.98 -0.46 0.43 0.34 -0.98 -1.07 -2.93 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -1.03 -0.98 0.26 0.55 -0.02 -0.98 -1.5 ... .. ..$ : num [1:20, 1:3] 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.. ..$ : num [1:20, 1:3] -4.88 -2.93 -2.24 -0.98 0.11 0.78 0.63 -0.43 -0.98 -2.93 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -1.38 -0.98 0.34 0.67 0.18 -0.98 -1.3 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -1.3 -0.98 0.18 0.67 0.34 -0.98 -1.38 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -0.98 -0.41 0.64 0.78 0.1 -0.98 -2.27 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -1.27 -0.98 0.06 0.55 0.06 -0.98 -1.27 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -2.49 -0.98 -0.17 0.52 0.38 -0.68 -0.98 -2.93 ... .. ..$ : num [1:22, 1:3] -6.84 -4.88 -2.93 -0.98 -0.92 0.67 0.98 1.04 0.98 0.55 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -0.98 0.22 0.98 1.27 1.33 0.98 0.63 ... .. ..$ : num [1:22, 1:3] -4.88 -2.93 -2.12 -0.98 0.34 0.98 1.38 1.26 0.98 0.11 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -0.98 -0.23 0.98 1.15 1.49 0.98 0.69 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -0.98 0.37 0.98 1.31 1.32 0.98 0.51 ... .. ..$ : num [1:20, 1:3] -6.84 -4.88 -2.93 -0.98 -0.34 0.92 0.98 1.26 0.98 0.46 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 -0.69 0.92 0.98 1.36 1.03 0.98 -0.43 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 -0.35 0.98 1.4 1.9 1.53 0.98 -0.13 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.08 0.98 1.7 2.16 1.82 0.98 0.39 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0 0.98 1.53 2.3 2.01 0.98 0.9 ... .. ..$ : num [1:20, 1:3] -2.93 -0.98 0 0.98 2.26 2.91 2.75 1.66 0.98 -0.98 ... .. ..$ : num [1:18, 1:3] -4.88 -2.93 -0.98 0.98 1.16 2.38 2.62 1.89 0.98 -0.12 ... .. ..$ : num [1:18, 1:3] -4.88 -2.93 -0.98 -0.17 0.98 1.82 2.39 2.16 1 0.98 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.57 0.98 2.07 2.38 1.77 0.98 0.1 ... .. ..$ : num [1:20, 1:3] -2.93 -0.98 0.08 0.98 1.9 2.38 2.07 0.98 0.57 -0.98 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.91 0.98 2.14 2.4 1.86 0.98 -0.11 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.98 1.16 2.3 2.38 1.61 0.98 -0.71 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0 0.98 1.79 2.26 1.95 0.98 0.45 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.52 0.98 1.85 2.15 1.66 0.98 -0.07 ... .. ..$ : num [1:22, 1:3] -2.93 -2.44 -0.98 0.98 1.28 2.33 2.26 1.4 0.98 -0.73 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.98 1.88 2.93 2.99 3.22 2.93 2.26 ... .. ..$ : num [1:22, 1:3] -2.93 -0.98 -0.02 0.98 2.7 2.93 3.43 3.38 2.93 2.4 ... .. ..$ : num [1:20, 1:3] -2.93 -0.98 0.84 0.98 2.87 2.93 3.63 3.33 2.93 1.89 ... .. ..$ : num [1:20, 1:3] -2.93 -0.98 0.98 1.88 2.93 3.45 3.56 2.93 2.62 0.98 ... .. ..$ : num [1:18, 1:3] -4.88 -2.93 -0.98 0.98 2.41 2.93 3.44 3.4 2.93 2.47 ... .. ..$ : num [1:20, 1:3] -4.88 -2.93 -0.98 0.98 2.34 2.93 3.63 3.56 2.93 2.38 ... .. ..$ : num [1:22, 1:3] -0.98 -0.37 0.98 2.5 2.93 3.63 3.56 2.93 2.38 0.98 ... .. ..$ : num [1:20, 1:3] -0.98 -0.37 0.98 2.64 2.93 3.43 3.4 2.93 2.47 0.98 ... .. ..$ : num [1:20, 1:3] -2.93 -0.98 0.37 0.98 2.75 2.93 3.56 3.33 2.93 2.01 ... .. .. [list output truncated] .. ..- attr(*, "dim")= int [1:2] 130 1 ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. ..@ patient : chr "" .. .. ..@ ID : chr "" .. .. ..@ structure.name : chr "" .. .. ..@ structure.volume: num 0 .. .. ..@ type : chr "cumulative" .. .. ..@ dose.max : num 0 .. .. ..@ dose.min : num 0 .. .. ..@ dose.mean : num 0 .. .. ..@ dose.median : num 0 .. .. ..@ dose.mode : num 0 .. .. ..@ dose.STD : num 0 .. .. ..@ conf.index : num 0 .. .. ..@ equiv.sphere : num 0 .. .. ..@ gradient : num 0 .. .. ..@ plan.sum : log FALSE .. .. ..@ dose.rx : num 0 .. .. ..@ dose.fx : num 0 .. .. ..@ rx.isodose : num 100 .. .. ..@ doses : num(0) .. .. ..@ dose.type : chr "absolute" .. .. ..@ dose.units : chr "cGy" .. .. ..@ volumes : num(0) .. .. ..@ volume.type : chr "relative"
The format for mandible is:
Formal class 'structure3D' [package "RadOnc"] with 9 slots ..@ name : chr "Mandible" ..@ volume : num 0 ..@ volume.units : chr "cc" ..@ coordinate.units: chr "cm" ..@ vertices : num [1:6994, 1:3] -12.7 -10.74 -8.79 -6.84 -4.88 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : chr [1:6994] "" "" "" "" ... .. .. ..$ : NULL ..@ origin : num [1:3] -1.93 -151.83 -122.85 ..@ triangles : num [1:3, 1:13984] 46 47 49 48 1 50 1 2 51 2 ... ..@ closed.polys :List of 104 .. ..$ : num [1:48, 1:3] -12.7 -10.74 -8.79 -6.84 -4.88 ... .. ..$ : num [1:52, 1:3] -14.65 -12.7 -10.74 -8.79 -6.84 ... .. ..$ : num [1:68, 1:3] -14.65 -12.7 -10.74 -8.79 -6.84 ... .. ..$ : num [1:74, 1:3] -14.65 -12.7 -10.74 -8.79 -6.84 ... .. ..$ : num [1:80, 1:3] -6.84 -6.51 -4.88 -2.93 -0.98 0.98 1.17 2.93 4.88 6.08 ... .. ..$ : num [1:90, 1:3] -10.74 -8.79 -6.84 -4.88 -2.93 ... .. ..$ : num [1:94, 1:3] -10.74 -8.79 -6.84 -4.88 -2.93 ... .. ..$ : num [1:98, 1:3] -10.74 -8.79 -6.84 -4.88 -2.93 ... .. ..$ : num [1:110, 1:3] 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[1:94, 1:3] -20.5 -18.6 -16.6 -14.7 -12.7 ... .. ..$ : num [1:94, 1:3] 12.7 14.7 15.5 16.6 17.3 ... .. ..$ : num [1:84, 1:3] -26.4 -24.4 -22.5 -20.9 -20.5 ... .. ..$ : num [1:94, 1:3] 14.7 15.3 16.6 17.4 18.6 ... .. ..$ : num [1:86, 1:3] -26.4 -24.4 -22.7 -22.5 -20.5 ... .. ..$ : num [1:90, 1:3] 12.7 14.7 16.6 18.3 18.6 ... .. ..$ : num [1:82, 1:3] -26.4 -24.4 -22.5 -22 -20.5 ... .. ..$ : num [1:80, 1:3] 22.5 24.4 24.8 26.4 26.9 ... .. ..$ : num [1:76, 1:3] -30.3 -28.3 -26.4 -24.4 -22.5 ... .. ..$ : num [1:78, 1:3] 20.5 22.5 24.4 26.1 26.4 ... .. ..$ : num [1:74, 1:3] -32.2 -30.3 -28.3 -26.4 -24.4 ... .. ..$ : num [1:74, 1:3] -32.2 -30.3 -28.3 -26.4 -24.4 ... .. ..$ : num [1:76, 1:3] 20.5 22.5 24.4 26.4 27.2 ... .. ..$ : num [1:72, 1:3] -32.2 -30.3 -28.3 -26.4 -24.6 ... .. ..$ : num [1:72, 1:3] 22.5 24.4 26.4 28.3 30.3 ... .. ..$ : num [1:72, 1:3] -32.2 -30.3 -28.3 -26.4 -25.6 ... .. ..$ : num [1:70, 1:3] 22.5 24.4 26.4 28.3 30.3 ... .. ..$ : num [1:68, 1:3] -36.1 -34.2 -32.2 -30.3 -28.3 ... .. ..$ : num [1:70, 1:3] 24.4 26.4 28.3 30.3 32.2 ... .. ..$ : num [1:70, 1:3] 30.3 32.2 34.2 36.1 38.1 ... .. ..$ : num [1:68, 1:3] -38.1 -36.1 -34.2 -32.8 -32.2 ... .. ..$ : num [1:66, 1:3] 34.2 36.1 37.7 38.1 39.3 ... .. ..$ : num [1:64, 1:3] -42 -40 -38.1 -36.1 -34.2 ... .. ..$ : num [1:66, 1:3] 36.1 36.8 38.1 38.7 39.8 ... .. ..$ : num [1:62, 1:3] -44 -42 -40 -38.1 -36.1 ... .. ..$ : num [1:64, 1:3] 36.1 36.8 38.1 39.2 40 ... .. ..$ : num [1:60, 1:3] -40 -38.1 -36.1 -34.7 -34.2 ... .. ..$ : num [1:62, 1:3] 36.1 36.6 38.1 39.5 40 ... .. ..$ : num [1:56, 1:3] -42 -40 -38.1 -36.1 -34.2 ... .. ..$ : num [1:62, 1:3] 36.1 36.3 38.1 39.3 40 ... .. ..$ : num [1:56, 1:3] -42 -40 -38.1 -36.1 -34.2 ... .. ..$ : num [1:60, 1:3] 34.2 36.1 38.1 39 40 ... .. ..$ : num [1:58, 1:3] -44 -42 -40 -38.7 -38.1 ... .. ..$ : num [1:58, 1:3] 34.2 36.1 38.1 38.8 40 ... .. ..$ : num [1:58, 1:3] -44 -42 -40 -39.4 -38.1 ... .. ..$ : num [1:58, 1:3] 34.2 36.1 38.1 39.2 40 ... .. ..$ : num [1:58, 1:3] -44 -42 -40 -39.4 -38.1 ... .. ..$ : num [1:56, 1:3] 36.1 38.1 38.9 40 40.3 ... .. ..$ : num [1:54, 1:3] -42 -41.9 -40 -39.6 -38.1 ... .. ..$ : num [1:56, 1:3] 36.1 38.1 39.6 40 40.6 ... .. ..$ : num [1:58, 1:3] -44 -42 -41.8 -40 -39.7 ... .. ..$ : num [1:56, 1:3] 36.1 38.1 39.7 40 40.9 ... .. ..$ : num [1:54, 1:3] -44 -42 -41.4 -40 -39.5 ... .. ..$ : num [1:58, 1:3] 36.1 38.1 38.9 40 40.3 ... .. ..$ : num [1:54, 1:3] -44 -42 -40.9 -40 -39.3 ... .. ..$ : num [1:58, 1:3] 36.1 38.1 39.3 40 40.4 ... .. ..$ : num [1:50, 1:3] -44 -42 -40.6 -40 -39.5 ... .. ..$ : num [1:54, 1:3] 36.1 38.1 39.5 40 41 ... .. ..$ : num [1:52, 1:3] -45.9 -44 -42 -40.1 -40 ... .. ..$ : num [1:52, 1:3] 38.1 39.9 40 41.4 41.9 ... .. ..$ : num [1:52, 1:3] -45.9 -44.8 -44 -42 -40 ... .. ..$ : num [1:54, 1:3] 38.1 38.4 40 40.6 41.7 ... .. ..$ : num [1:52, 1:3] -45.9 -44 -42 -41.9 -40.1 ... .. ..$ : num [1:54, 1:3] 38.1 39.9 40 41 41.8 ... .. ..$ : num [1:48, 1:3] -45.9 -44 -42.2 -42 -40.8 ... .. ..$ : num [1:52, 1:3] 38.1 40 40.7 41.6 42 ... .. ..$ : num [1:48, 1:3] -45.9 -44 -42.4 -42 -41.5 ... .. ..$ : num [1:54, 1:3] 38.1 39.1 40 41.3 42 ... .. ..$ : num [1:48, 1:3] -45.9 -44.1 -44 -42.6 -42.6 ... .. ..$ : num [1:54, 1:3] 38.1 40 40.5 41.8 42 ... .. ..$ : num [1:48, 1:3] -45.9 -44 -43.4 -42.7 -42.6 ... .. ..$ : num [1:54, 1:3] 38.1 40 41.3 42 42.1 ... .. ..$ : num [1:52, 1:3] -45.9 -44.2 -44 -43.1 -43.1 ... .. ..$ : num [1:22, 1:3] 40 40.2 41.9 42 43 ... .. ..$ : num [1:22, 1:3] -45.9 -44 -43.6 -43 -43.1 ... .. ..$ : num [1:24, 1:3] 45.9 47.5 47.8 47.9 49.2 ... .. ..$ : num [1:24, 1:3] -49.8 -47.9 -47.4 -46.8 -46.7 ... .. ..$ : num [1:16, 1:3] 40 40.8 42 42.4 43.2 ... .. ..$ : num [1:22, 1:3] -45.9 -45.5 -44 -43.8 -43.5 ... .. ..$ : num [1:26, 1:3] 45.9 46.4 47.9 48.1 49.3 ... .. ..$ : num [1:22, 1:3] -49.8 -47.9 -47.8 -46.8 -46.2 ... .. ..$ : num [1:12, 1:3] 40 41.7 42 42.6 43.2 ... .. ..$ : num [1:18, 1:3] -47.9 -45.9 -44.5 -44 -44.1 ... .. ..$ : num [1:24, 1:3] 45.9 47.9 48.2 49.4 49.8 ... .. ..$ : num [1:22, 1:3] -49.8 -49.5 -47.9 -47.1 -46.2 ... .. ..$ : num [1:12, 1:3] 40 41.3 42 43 43.4 ... .. ..$ : num [1:18, 1:3] -47.9 -45.9 -44.9 -44.5 -44.5 ... .. ..$ : num [1:24, 1:3] 47.9 48.5 49.6 49.8 50.8 ... .. .. [list output truncated] .. ..- attr(*, "dim")= int [1:2] 104 1 ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. ..@ patient : chr "" .. .. ..@ ID : chr "" .. .. ..@ structure.name : chr "" .. .. ..@ structure.volume: num 0 .. .. ..@ type : chr "cumulative" .. .. ..@ dose.max : num 0 .. .. ..@ dose.min : num 0 .. .. ..@ dose.mean : num 0 .. .. ..@ dose.median : num 0 .. .. ..@ dose.mode : num 0 .. .. ..@ dose.STD : num 0 .. .. ..@ conf.index : num 0 .. .. ..@ equiv.sphere : num 0 .. .. ..@ gradient : num 0 .. .. ..@ plan.sum : log FALSE .. .. ..@ dose.rx : num 0 .. .. ..@ dose.fx : num 0 .. .. ..@ rx.isodose : num 100 .. .. ..@ doses : num(0) .. .. ..@ dose.type : chr "absolute" .. .. ..@ dose.units : chr "cGy" .. .. ..@ volumes : num(0) .. .. ..@ volume.type : chr "relative"
The format for teeth is:
Formal class 'structure.list' [package "RadOnc"] with 1 slots ..@ structures:List of 3 .. ..$ Tooth #1:Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. ..@ name : chr "Tooth #1" .. .. .. ..@ volume : num 0 .. .. .. ..@ volume.units : chr "cc" .. .. .. ..@ coordinate.units: chr "cm" .. .. .. ..@ vertices : num [1:324, 1:3] -28.3 -26.4 -24.4 -23.4 -22.5 ... .. .. .. ..@ origin : num [1:3] -25.2 -129.3 -100.7 .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. ..@ closed.polys :List of 23 .. .. .. .. ..$ : num [1:14, 1:3] -28.3 -26.4 -24.4 -23.4 -22.5 ... .. .. .. .. ..$ : num [1:20, 1:3] -28.3 -26.4 -25.8 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -30.3 -28.3 -26.4 -24.4 -24.1 ... .. .. .. .. ..$ : num [1:24, 1:3] -30.3 -28.3 -26.4 -24.4 -24.4 ... .. .. .. .. ..$ : num [1:22, 1:3] -30.3 -28.3 -26.4 -24.4 -23.4 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -27.5 -26.4 -24.4 -23.1 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -26.2 -24.4 -22.8 ... .. .. .. .. ..$ : num [1:20, 1:3] -28.3 -26.4 -25.3 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:30, 1:3] -28.3 -27.9 -26.4 -24.4 -24.1 ... .. .. .. .. ..$ : num [1:12, 1:3] -28.3 -26.6 -26.4 -24.4 -24 ... .. .. .. .. ..$ : num [1:10, 1:3] -30.3 -28.3 -26.9 -26.4 -25 ... .. .. .. .. ..$ : num [1:10, 1:3] -22.5 -20.5 -18.6 -17.9 -18.1 ... .. .. .. .. ..$ : num [1:10, 1:3] -28.3 -28.2 -26.4 -24.4 -23.9 ... .. .. .. .. ..$ : num [1:10, 1:3] -30.3 -28.3 -26.4 -25.6 -25.3 ... .. .. .. .. ..$ : num [1:8, 1:3] -20.5 -18.6 -17 -17.6 -18.6 ... .. .. .. .. ..$ : num [1:16, 1:3] -28.3 -26.4 -25 -24.5 -26.3 ... .. .. .. .. ..$ : num [1:8, 1:3] -20.5 -18.6 -17.4 -18.1 -18.6 ... .. .. .. .. ..$ : num [1:14, 1:3] -28.3 -26.4 -25.1 -26.3 -26.4 ... .. .. .. .. ..$ : num [1:6, 1:3] -18.6 -17.3 -18.3 -18.6 -20.4 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -28.3 -27.4 -28.3 -30.3 ... .. .. .. .. ..$ : num [1:4, 1:3] -18.6 -17.3 -18.6 -19.7 -128.7 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -28.3 -27.5 -28.3 -30.3 ... .. .. .. .. ..$ : num [1:6, 1:3] -18.6 -17.4 -16.8 -18.6 -20.4 ... .. .. .. .. ..- attr(*, "dim")= int [1:2] 23 1 .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. ..@ structure.name : chr "" .. .. .. .. .. ..@ structure.volume: num(0) .. .. .. .. .. ..@ type : chr "cumulative" .. .. .. .. .. ..@ dose.max : num 0 .. .. .. .. .. ..@ dose.min : num 0 .. .. .. .. .. ..@ dose.mean : num 0 .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. ..@ dose.rx : num 0 .. .. .. .. .. ..@ dose.fx : num 0 .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. ..@ doses : num(0) .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. ..@ dose.units : chr "cGy" .. .. .. .. .. ..@ volumes : num(0) .. .. .. .. .. ..@ volume.type : chr "relative" .. ..$ Tooth #2:Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. ..@ name : chr "Tooth #2" .. .. .. ..@ volume : num 0 .. .. .. ..@ volume.units : chr "cc" .. .. .. ..@ coordinate.units: chr "cm" .. .. .. ..@ vertices : num [1:338, 1:3] -26.4 -26.2 -24.4 -23.5 -22.5 ... .. .. .. ..@ origin : num [1:3] -25.1 -129.4 -100.9 .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. ..@ closed.polys :List of 24 .. .. .. .. ..$ : num [1:16, 1:3] -26.4 -26.2 -24.4 -23.5 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -25.8 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:24, 1:3] -30.3 -28.3 -26.4 -24.5 -24.4 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.4 -23.9 -22.5 ... .. .. .. .. ..$ : num [1:24, 1:3] -30.3 -28.3 -26.4 -24.4 -22.8 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -27.1 -26.4 -24.4 -23.2 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -26.4 -25.9 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:24, 1:3] -30.3 -28.3 -26.4 -25 -24.4 ... .. .. .. .. ..$ : num [1:18, 1:3] -28.3 -26.4 -24.7 -24.4 -22.8 ... .. .. .. .. ..$ : num [1:10, 1:3] -22.5 -20.5 -18.6 -17.8 -18.6 ... .. .. .. .. ..$ : num [1:14, 1:3] -28.3 -26.4 -26.3 -24.6 -24.4 ... .. .. .. .. ..$ : num [1:10, 1:3] -30.3 -28.3 -26.6 -26.4 -25.7 ... .. .. .. .. ..$ : num [1:10, 1:3] -22.5 -20.5 -18.6 -17.9 -18.3 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -27.5 -26.4 -24.6 -24.4 ... .. .. .. .. ..$ : num [1:8, 1:3] -20.5 -18.6 -16.9 -16.8 -18.6 ... .. .. .. .. ..$ : num [1:10, 1:3] -28.3 -26.4 -24.4 -24.2 -24.3 ... .. .. .. .. ..$ : num [1:8, 1:3] -30.3 -28.3 -27 -26.4 -28.3 ... .. .. .. .. ..$ : num [1:10, 1:3] -20.5 -18.6 -16.6 -16.3 -16.4 ... .. .. .. .. ..$ : num [1:6, 1:3] -28.3 -26.4 -25.3 -26.4 -28.3 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -28.3 -27.1 -28.3 -30.3 ... .. .. .. .. ..$ : num [1:6, 1:3] -18.6 -17.1 -17.6 -18.6 -18.6 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -28.3 -26.9 -28.3 -30.3 ... .. .. .. .. ..$ : num [1:8, 1:3] -18.6 -18.5 -16.6 -16.4 -16.6 ... .. .. .. .. ..$ : num [1:4, 1:3] -18.6 -16.8 -18.6 -19.1 -129.4 ... .. .. .. .. ..- attr(*, "dim")= int [1:2] 24 1 .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. ..@ structure.name : chr "" .. .. .. .. .. ..@ structure.volume: num(0) .. .. .. .. .. ..@ type : chr "cumulative" .. .. .. .. .. ..@ dose.max : num 0 .. .. .. .. .. ..@ dose.min : num 0 .. .. .. .. .. ..@ dose.mean : num 0 .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. ..@ dose.rx : num 0 .. .. .. .. .. ..@ dose.fx : num 0 .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. ..@ doses : num(0) .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. ..@ dose.units : chr "cGy" .. .. .. .. .. ..@ volumes : num(0) .. .. .. .. .. ..@ volume.type : chr "relative" .. ..$ Tooth #3:Formal class 'structure3D' [package "RadOnc"] with 9 slots .. .. .. ..@ name : chr "Tooth #3" .. .. .. ..@ volume : num 0 .. .. .. ..@ volume.units : chr "cc" .. .. .. ..@ coordinate.units: chr "cm" .. .. .. ..@ vertices : num [1:310, 1:3] -28.3 -26.4 -28.3 -29.4 -24.4 ... .. .. .. ..@ origin : num [1:3] -24.7 -129.4 -100.3 .. .. .. ..@ triangles : logi[1:3, 0 ] .. .. .. ..@ closed.polys :List of 24 .. .. .. .. ..$ : num [1:4, 1:3] -28.3 -26.4 -28.3 -29.4 -126.7 ... .. .. .. .. ..$ : num [1:6, 1:3] -24.4 -22.5 -22 -22.5 -24.4 ... .. .. .. .. ..$ : num [1:16, 1:3] -28.3 -26.4 -24.4 -24 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.4 -24.1 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.4 -23.6 -22.5 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -26.4 -24.4 -23.4 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.4 -23 -22.5 ... .. .. .. .. ..$ : num [1:24, 1:3] -28.3 -26.4 -25.2 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.7 -24.4 -22.5 ... .. .. .. .. ..$ : num [1:22, 1:3] -28.3 -26.4 -24.4 -24.2 -22.9 ... .. .. .. .. ..$ : num [1:14, 1:3] -28.3 -26.4 -24.4 -23.6 -24 ... .. .. .. .. ..$ : num [1:10, 1:3] -22.5 -20.5 -18.6 -16.8 -17.6 ... .. .. .. .. ..$ : num [1:8, 1:3] -28.3 -26.4 -24.4 -23.5 -24.4 ... .. .. .. .. ..$ : num [1:8, 1:3] -28.3 -26.4 -26 -25.4 -26.4 ... .. .. .. .. ..$ : num [1:10, 1:3] -20.5 -18.6 -16.6 -16.5 -16.6 ... .. .. .. .. ..$ : num [1:10, 1:3] -28.3 -27.3 -26.4 -24.4 -24.2 ... .. .. .. .. ..$ : num [1:8, 1:3] -30.3 -28.3 -26.4 -26.3 -26.4 ... .. .. .. .. ..$ : num [1:10, 1:3] -20.5 -18.6 -16.6 -16.5 -16.6 ... .. .. .. .. ..$ : num [1:16, 1:3] -28.3 -27.3 -26.4 -25.4 -26.4 ... .. .. .. .. ..$ : num [1:8, 1:3] -20.5 -18.6 -16.7 -17.7 -18.6 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -28.3 -27.2 -28.3 -30.3 ... .. .. .. .. ..$ : num [1:6, 1:3] -18.6 -18 -17.6 -18.6 -20.1 ... .. .. .. .. ..$ : num [1:6, 1:3] -30.3 -29.7 -28.7 -30.3 -30.6 ... .. .. .. .. ..$ : num [1:6, 1:3] -18.6 -16.7 -16.7 -18.6 -18.7 ... .. .. .. .. ..- attr(*, "dim")= int [1:2] 24 1 .. .. .. ..@ DVH :Formal class 'DVH' [package "RadOnc"] with 18 slots .. .. .. .. .. ..@ patient : chr "" .. .. .. .. .. ..@ ID : chr "" .. .. .. .. .. ..@ structure.name : chr "" .. .. .. .. .. ..@ structure.volume: num(0) .. .. .. .. .. ..@ type : chr "cumulative" .. .. .. .. .. ..@ dose.max : num 0 .. .. .. .. .. ..@ dose.min : num 0 .. .. .. .. .. ..@ dose.mean : num 0 .. .. .. .. .. ..@ dose.median : num 0 .. .. .. .. .. ..@ dose.mode : num 0 .. .. .. .. .. ..@ dose.STD : num 0 .. .. .. .. .. ..@ conf.index : num 0 .. .. .. .. .. ..@ equiv.sphere : num 0 .. .. .. .. .. ..@ gradient : num 0 .. .. .. .. .. ..@ plan.sum : log FALSE .. .. .. .. .. ..@ dose.rx : num 0 .. .. .. .. .. ..@ dose.fx : num 0 .. .. .. .. .. ..@ rx.isodose : num 100 .. .. .. .. .. ..@ doses : num(0) .. .. .. .. .. ..@ dose.type : chr "absolute" .. .. .. .. .. ..@ dose.units : chr "cGy" .. .. .. .. .. ..@ volumes : num(0) .. .. .. .. .. ..@ volume.type : chr "relative"
The format for stomach is:
Formal class 'zDVH' [package "RadOnc"] with 22 slots ..@ patient : chr "" ..@ ID : chr "" ..@ structure.name : chr "STOMACH" ..@ structure.volume: num 699 ..@ type : chr "differential" ..@ dose.max : num 53.6 ..@ dose.min : num 0.594 ..@ dose.mean : num 12.5 ..@ dose.median : num 0 ..@ dose.mode : num 0 ..@ dose.STD : num 0 ..@ conf.index : num 0 ..@ equiv.sphere : num 0 ..@ gradient : num 0 ..@ plan.sum : log FALSE ..@ dose.rx : num 55 ..@ dose.fx : num 25 ..@ rx.isodose : num 100 ..@ doses : num [1:114] 0.125 0.5 1 1.5 2 2.5 3 3.5 4 4.5 ... ..@ dose.type : chr "absolute" ..@ dose.units : chr "Gy" ..@ volumes : numeric [1:114, 1:48] 0 0 0 0 0 ... .. ..- attr(*, "dimnames")=List of 2 .. .. ..$ : NULL .. .. ..$ : chr [1:48] "-96" "-93" "-90" "-87" ... .. ..- attr(*, "class")= chr [1:2] "numeric" "matrix" ..@ volume.type : chr "absolute"
data(list="RadOnc",package="RadOnc")data(list="RadOnc",package="RadOnc")
Function to extract three-dimensional structural and dosimetric data from input file(s) in DICOM-RT format
read.DICOM.RT(path, exclude=NULL, recursive=TRUE, verbose=TRUE, limit=NULL, DVH=TRUE, zDVH=FALSE, modality="CT", ...)read.DICOM.RT(path, exclude=NULL, recursive=TRUE, verbose=TRUE, limit=NULL, DVH=TRUE, zDVH=FALSE, modality="CT", ...)
path |
Location of directory containing relevant DICOM-RT information |
exclude |
Character string specifying exclusion criteria used to skip processing of specific file(s) within the DICOM-RT directory. |
recursive |
Logical (default is |
verbose |
Logical value (default is |
limit |
Numerical value specifying size threshold over which to skip processing of specific structures (number corresponds to the number of points used to define each structure surface) |
DVH |
Logical value (default is |
zDVH |
Logical value (default is |
modality |
Parameter used to specify the scan type expected in importing DICOM-RT data (must be one one of |
... |
Additional parameters passed to |
Returns a single structure.list object containing all structures from input DICOM-RT file(s)
Reid F. Thompson ([email protected])
readDICOM, structure.list, structure3D
Function to extract DVH data from input file(s). Supported file formats include Aria (v8-13), DICOM-RT, CadPlan, Monaco, RayStation, and TomoTherapy.
read.DVH(file, type=NA, verbose=TRUE, collapse=TRUE, modality=NULL, encoding="latin1")read.DVH(file, type=NA, verbose=TRUE, collapse=TRUE, modality=NULL, encoding="latin1")
file |
Location of file containing relevant DVH information. One or more files may be specified. If multiple files are specified, all will be imported simultaneously. |
type |
Character vector specifying the DVH file format corresonding to each element in |
verbose |
Single logical value indicating whether or not to output verbose information and status in text |
collapse |
Single logical value indicating whether or not to collapse input from multiple files into a single |
modality |
When |
encoding |
Character value specifying the encoding type for the DVH file (default is |
Returns a single DVH.list object containing all DVH information from a single input file. If multiple files are specified, a list of DVH.list objects will be returned.
Reid F. Thompson ([email protected])
# Read two DVH example files file1 <- system.file("extdata/John_Doe.dvh", package="RadOnc") johndoe <- read.DVH(file=file1, type="aria10", verbose=TRUE) file2 <- system.file("extdata/Jane_Doe.dvh", package="RadOnc") janedoe <- read.DVH(file=file2, type="aria10", verbose=TRUE) combined <- read.DVH(file=c(file1, file2), type="aria10", collapse=TRUE)# Read two DVH example files file1 <- system.file("extdata/John_Doe.dvh", package="RadOnc") johndoe <- read.DVH(file=file1, type="aria10", verbose=TRUE) file2 <- system.file("extdata/Jane_Doe.dvh", package="RadOnc") janedoe <- read.DVH(file=file2, type="aria10", verbose=TRUE) combined <- read.DVH(file=c(file1, file2), type="aria10", collapse=TRUE)
"RTdata"
A data structure containing a corresponding CT image, dose grid, and structure set
Objects can be created by calls of the form new("RTdata", name, CT, dose, structures, ...).
name:Name of the dataset (e.g. "Patient XX")
CT:Object of class "array" containing computed tomography (CT) image data in Houndsfield units
dose:Object of class "array" containing dose grid data (pre-calculated using a separate treatment planning system) with a "dose.units" attribute specifying the units of dose.
structures:Object of class "structure.list" containing the corresponding structure set, indexed to the CT and dose grid coordinate systems
Extract a given parameter from a RTdata object
Assign a value to a given parameter within a RTdata object
Extract dataset name from an RTdata object
Assign a name to an RTdata object
Display summary of RTdata object
Display summary of RTdata object
Reid F. Thompson ([email protected])
showClass("RTdata")showClass("RTdata")
"structure.list"
A data structure containing one or more 3D structure (structure3D) objects
Objects can be created by calls of the form new("structure.list", structures, ...).
structures:List of structure3D objects
Extract subset of structure list (regular expressions may be specified if desired, see regex for more details)
Extract single structure3D object from structure list
Replace single structure3D object in structure list
Extract parameter(s) from structure3D objects within structure list
Convert a structure.list object to a list containing individual structure3D objects. Note that the reverse conversion can be performed using the as command and specifying class="structure.list".
Combine two or more structure lists and/or structure3D objects
Apply function to a list of structure3D objects
Extract number of structure3D objects in structure list
Extract structure names for structure3D objects in structure list
Assign structure name(s) to one or more structure3D objects in structure list
Display summary of structure list
Compute the range (minimum and maximum coordinates) containing all structure3D ojbects in structure list
Return a structure list whose structure3D objects are in reverse order
Display summary of structure list
Reid F. Thompson ([email protected])
# Description of structure/slots in class showClass("structure.list")# Description of structure/slots in class showClass("structure.list")
"structure3D"
A data structure containing 3D volumetric (structure3D) data and associated parameters for a single structure object
Objects can be created by calls of the form new("structure3D", name, volume, volume.units, coordinate.units, vertices, origin, triangles, DVH).
name:Name of the structure (e.g. "Stomach")
volume:Volume of the structure (in volume.units)
volume.units:A character string specifying the units of volume (must be "cc")
coordinate.units:A character string specifying the units of the coordinate system (must be one of "cm" or "mm")
vertices:Specifies all points defining the given structure, with data contained in a Nx3 matrix where each column represents x, y, and z coordinates, respectively, for each of N points
origin:A numeric vector containing the x, y, and z coordinates corresponding to the center of the structure
triangles:Specifies a complete combination of points which define the triangular mesh surface of the structure; data is contained in a 3xN matrix where each row represents one of the three vertices of a each triangle within the mesh, with N columns corresponding to the number of triangles; note that the value of each element in triangles references a point in vertices, such that all values in triangles must be between 1 and dim(vertices)[1]
closed.polys:Specifies a complete set of axially-defined closed polygons which, together, comprise the surface of the structure; data is contained in a list of Nx3 matrices where each row represents the x, y, and z coordinates of a point in a single polygon
DVH:Object of class DVH
Extract a given parameter from a structure3D object
Assign a value to a given parameter within a structure3D object
Combine multiple structure3D objects into a single structure.list
Extract dimensions (number of vertices and axial slices) from structure3D object
Extract structure name from structure3D object
Assign structure name to a structure3D object
Display summary of structure3D object
Extract coordinate range from structure3D object
Display summary of structure3D object
Reid F. Thompson ([email protected])
# Description of structure/slots in class showClass("structure3D")# Description of structure/slots in class showClass("structure3D")
This function is designed to isolate one or more structure(s) from a list of DVH lists according to user input.
## S3 method for class 'DVH.list' subset(x, structure, patient, ID, constraint, ignore.case=TRUE, select)## S3 method for class 'DVH.list' subset(x, structure, patient, ID, constraint, ignore.case=TRUE, select)
x |
Represents a |
structure |
Vector used to sub-select structures from |
patient |
Vector used to sub-select specific patient data from |
ID |
Vector used to sub-select specific patient data from |
constraint |
Vector of one or more dosimetric constraints to apply to |
ignore.case |
Logical value specifying whether or not to use case-sensitive pattern matching; if |
select |
Must be one of |
Returns a single DVH list
Reid F. Thompson ([email protected])
data(list="RadOnc", package="RadOnc") subset(johndoe, structure="kidney", constraint="Dmean < 500(cGy)", ignore.case=TRUE) subset(johndoe, constraint="volume > 200(cc)")data(list="RadOnc", package="RadOnc") subset(johndoe, structure="kidney", constraint="Dmean < 500(cGy)", ignore.case=TRUE) subset(johndoe, constraint="volume > 200(cc)")
"zDVH"
A data structure containing axially-segmented Dose-Volume Histogram (zDVH) data and associated parameters for a single structure
Objects can be created by calls of the form new("zDVH", patient, structure.name, structure.volume, type, dose.max, dose.min, dose.mean, dose.median, dose.mode, dose.STD, conf.index, equiv.sphere, gradient, dose.rx, dose.fx, doses, dose.type, dose.units, volumes, volume.type, ...).
patient:Name of the patient (e.g. "Jane Doe")
ID:Additional patient identifier or medical record number (e.g. "123456789")
structure.name:Name of the structure (e.g. "Stomach")
structure.volume:Volume of the structure (in cubic centimeters)
type:A character string specifying the DVH type (must be one of "cumulative" or "differential")
dose.max:Maximum (point) dose contained within the structure
dose.min:Minimum dose contained within the structure
dose.mean:Mean dose to the structure
dose.median:Median dose to the structure
dose.mode:Modal dose to the structure
dose.STD:Standard deviation of dose to the structure
conf.index:Conformality index
equiv.sphere:Equivalent sphere (diameter in centimeters)
gradient:Dose gradient (in centimeters)
dose.rx:Prescription dose (in units specified by dose.units)
dose.fx:Fractional dose (in units specified by dose.units)
rx.isodose:Isodose line (%) receiving prescription dose (default is 100%)
doses:List of doses corresponding to "volumes"
dose.type:A character string specifying the dose type (must be one of "relative" or "absolute")
dose.units:A character string specifying the dose units (must be one of "cGy" or "Gy")
volumes:Matrix containing NxM dimensions, with N=length(doses) and M representing the number of axial segments for which of each a DVH was obtained
volume.type:A character string specifying the volume type (must be one of "relative" or "absolute")
Extract dose or volume parameter(s) from zDVH object. Only one parameter may be specified at a time. Parameter specification should be of the form ["<A><B><C>"]: <A> is equivalent to "V" or "D", representing a volume or dose, respectively; <B> usually denotes a numerical value specifying the dose or volume; and <C> represents the dose or volume units ("cGy", "Gy", "%", or "cc"). An example would be ["V20Gy"] which represents the volume of the structure receiving at least 20Gy dose. Specialized dosimetric keywords may also be used: "Dmax" (maximum dose), "Dmin" (minimum dose), "Dmean" (mean dose), "Dintegral" (estimated integral dose), "DRx" (prescription dose), and "volume" (total structure volume). If an improper parameter is specified however, NA results will be returned. See package documentation (vignette) for more details.
Extract a given parameter from a zDVH object
Assign a value to a given parameter within a zDVH object
Combine multiple zDVH objects into a single list
Extract maximum dose from zDVH object
Extract mean dose from zDVH object
Extract minimum dose from zDVH object
Extract structure name from zDVH object
Assign structure name to zDVH object
Display summary of zDVH object
Extract dose range from zDVH object
Display summary of zDVH object
Compute the total (summed) DVH from two or more zDVH and/or DVH objects. Note that structures are assumed to be non-overlapping; any overlaps in structure volumes may generate inaccurate dose summation.
Reid F. Thompson ([email protected])
# Description of structure/slots in class showClass("zDVH")# Description of structure/slots in class showClass("zDVH")