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espadon (version 1.11.3)

Easy Study of Patient DICOM Data in Oncology

Description

Exploitation, processing and 2D-3D visualization of DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, in a patient-oriented perspective.

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Version

Install

install.packages('espadon')

Monthly Downloads

283

Version

1.11.3

License

GPL-3

Maintainer

Cathy Fontbonne

Last Published

November 17th, 2025

Functions in espadon (1.11.3)

bin.closing

Binary volume closing
bin.clustering

Binary volume clustering
Rdcm.upgrade

Updating Rdcm files.
Rdcm.inventory

Inventory of espadon objects from Rdcm files
add.shape

Adding shape to a 3D volume.
add.margin

Adding or removing a margin to a volume
bin.dilation

Binary volume dilation
bin.cuboid

Create a volume containing predefined shapes
bin.from.roi

Creation of a binary volume according to RoI
bin.erosion

Binary volume erosion
dicom.browser

DICOM raw data browser
castlow.str

Cast of a character string
bin.opening

Binary volume opening
castup.str

Cast of a character string
bin.subtraction

Subtraction of two binaries
bin.inversion

Inversion of a binary
bin.intersection

Intersection of two binaries
dicom.parser

Conversion of DICOM raw data into a dataframe or a list of DICOM TAG information
bin.from.vol

Creation of a binary volume according to the voxel values of a volume
bin.sum

Sum of two binaries
dicom.patient.anonymiser

Anonymisation of a patient's DICOM files
dicom.to.Rdcm.converter

Conversion of DICOM object into files that can be interpreted by the espadon package
dicom.viewer

DICOM content viewer
display.2D.histo

Display of a 2D histogram
dicom.tag.dictionary

DICOM TAG dictionary
dicom.set.tag.value

Change TAG value in DICOM raw data
dicom.tag.parser

DICOM TAG parser
dicom.raw.data.loader

DICOM file loading in raw data
display.legend

Display of the RoI legend
display.3D.contour

Display the 3D contours of the RoI
display.kplane

Display of a plane of a volume
display.obj.links

Display patient objects links
display.histo

Display of the counts of a histogram
dicom.raw.data.anonymizer

DICOM anonymizer
display.3D.mesh

3D display of a mesh
display.3D.sections

Display 3D sections of a patient
display.DVH.pc

Display of a cumulative DVH in percent of total volume
display.dV_dx

Display of the volume density of a histogram
display.3D.stack

Display in 3D the selected planes of an espadon class volume
display.DVH

Display of a DVH
fan.beam

Creation of pyramid fan object with constant angle step.
fan.planar

Creation of pyramid fan object passing through pixels of a plane.
espadon.class

ESPADON class
espadon-package

espadon: Easy Study of Patient DICOM Data in Oncology
err.metrics.from.roi

Error evaluation metrics for 2-volume comparisons
export

Export espadon objects in DICOM format
fan.to.voxel

Indices of voxels crossed by a fan
fan.sphere

Creation of spherical fan object.
display.palette

Display of the color scale of a color palette
display.plane

Display the transverse frontal or sagittal view in the patient reference system
get.obj.connection

List of connections between objects
get.extreme.pt

Coordinates of the extreme points
get.ijk.from.xyz

Indices relating to the coordinates of the points
get.roi.connection

List of inter-connections between RoI
get.value.from.ijk

Value of the volume at a selection of DICOM indices
get.line

Image value along an axis
get.rigid.M

Transfer matrix between two frames of reference
get.plane

Extracting a plane from a volume
get.value.from.mesh

Voxel value at a given depth of a mesh
get.ijk.from.index

Conversion of the indices of a point into ijk vector
histo.from.roi

Histogram according to a RoI
get.volume.from.roi

Volume of a region of interest (RoI)
histo.vol

Histogram of a volume
get.xyz.from.index

Conversion of the indices of a point, into xyz coordinate vector in the patient's frame of reference
histo.DVH

Cumulative Dose Volume Histogram
histo.from.bin

Histogram according to a binary
get.value.from.xyz

Voxel values on a selection of points
histo.2D

2D histograms of 2 volumes
grid.equal

Comparison of the grids of two volume objects
get.volume.from.bin

Volume selected by binary volume
load.patient.from.dicom

Loading patient data from DICOM files
mesh.from.bin

Creation of a mesh according to a binary volume
mesh.repair

Repair of a mesh
load.obj.data

Load data of an espadon class object
load.obj.from.Rdcm

Loading an espadon object from *.Rdcm file
load.Rdcm.raw.data

Loading a *.Rdcm file
mesh.in.new.ref

Change of frame of reference of a mesh
load.T.MAT

Loading of information about transfer matrices between frames of reference of patient Rdcm objects.
pal.rainbow

Rainbow palette
pal.RVV

Conversion of Hounsfied Units to Realistic Volume Vizualization colors
load.obj.from.dicom

Loading an espadon object from DICOM files or folder
load.patient.from.Rdcm

Loading patient data from *.Rdcm files
nesting.bin

Restrict volume to a binary selection
mesh.spheric.proj

Adding spherical coordinates to a mesh
orientation.create

Creation of orientation
obj.create

Espadon object creating
rt.gamma.index

Gamma index 2D - 3D
save.to.Rdcm

Save a espadon object in a pre-formatted *.Rdcm file
nesting.cube

Restriction of a volume to a rectangular parallelepiped
plot

plot a 2D cut of a 3D object
ref.add

Adding a frame of reference in T.MAT
nesting.roi

Restrict volume to RoI
save.T.MAT

Save a T.MAT class object
ref.remove

Deletion of a frame of reference in T.MAT
ref.cutplane.add

Adding volume's cutting planes frame of reference in T.MAT
rt.indices.from.bin

Dosimetry, volume, conformity, homogeneity indices from binary selection
rt.indices.from.roi

Dosimetry, volume, conformity, homogeneity indices from RoI
ref.srctodest.add

Linking two existing frames of reference in T.MAT
rt.chi.index

Chi index 2D - 3D
struct.create

Struct creating from contours list
sp.similarity.from.bin

Volume-based spatial similarity metrics calculated from binary modality 3D volumes.
struct.from.bin

Creation of struct class object from a binary volume
select.names

Regions of Interest (RoI) indices
struct.update_roiinfo

Update roi.info
struct.merge

Merging of structures into a new structure
set.reference.obj

Set the reference objects of a espadon object
toy.load.patient

Load a toy patient for test
vector.product

Vector product of two vectors
vol.gradient

Gradient of a volume
vol.from.bin

Volume class object according to binary selection
struct.from.mesh

Creation of struct class object from an espadon mesh
struct.in.new.ref

Change of frame of reference of a "struct" class object.
vol.subsampling

Subsampling a volume
vol.error

Error volume
vol.median

Median filter on a volume
vol.create

Volume creating
vol.in.new.ref

Change of frame of reference of a volume
toy.dicom.raw

toy DICOM raw data
xlsx.from.dcm

Converting DICOM files to .xlsx files
vol.sum

Sum of 2 volumes
vol.repair

repairing missing planes of volumes
xlsx.from.Rdcm

Converting .Rdcm files to .xlsx files
study.deployment

Deployment of DICOM files from multiple patients
struct.clustering

Clustering volumes by RoI
vol.regrid

Transform the grid of a volume class object into the grid of another
vol.oversampling

Oversampling a volume
sp.similarity.from.mesh

Distance-based spatial similarity metrics calculated from the mesh.
vol.abserror

Absolute error volume
vol.copy

Creating a volume from another one