Package: espadon 1.11.5

Cathy Fontbonne

espadon: Easy Study of Patient DICOM Data in Oncology

Read, process, and export DICOM and DICOM-RT files (structures, dosimetry, imagery) for medical physics and clinical research, with patient-oriented 2D-3D visualization.

Authors:Cathy Fontbonne [aut, cre], Jean-Marc Fontbonne [aut], Nathan Azemar [ctb]

espadon_1.11.5.tar.gz
espadon_1.11.5.tar.gz(r-4.7-arm64)espadon_1.11.5.tar.gz(r-4.7-x86_64)espadon_1.11.5.tar.gz(r-4.6-arm64)espadon_1.11.5.tar.gz(r-4.6-x86_64)
espadon_1.11.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
espadon/json (API)

# Install 'espadon' in R:

install.packages('espadon', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.30 score 5 scripts 427 downloads 130 exports 70 dependencies

Last updated from:fd2f797638. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	312
linux-devel-x86_64	OK	336
source / vignettes	OK	381
linux-release-arm64	OK	292
linux-release-x86_64	OK	336
wasm-release	OK	229

Exports:add.margin add.shape bin.closing bin.clustering bin.cuboid bin.cylinder bin.dilation bin.ellipsoid bin.erosion bin.from.roi bin.from.vol bin.intersection bin.inversion bin.opening bin.subtraction bin.sum castlow.str castup.str dicom.browser dicom.parser dicom.patient.anonymiser dicom.raw.data.anonymizer dicom.raw.data.loader dicom.set.tag.value dicom.tag.dictionary dicom.tag.parser dicom.to.Rdcm.converter dicom.viewer display.2D.histo display.3D.contour display.3D.mesh display.3D.sections display.3D.stack display.dV_dx display.DVH display.DVH.pc display.histo display.kplane display.legend display.obj.links display.palette display.plane err.metrics.from.bin err.metrics.from.roi espadon.class export fan.beam fan.planar fan.sphere fan.to.voxel get.extreme.pt get.ijk.from.index get.ijk.from.xyz get.line get.obj.connection get.plane get.rigid.M get.roi.connection get.value.from.ijk get.value.from.mesh get.value.from.xyz get.volume.from.bin get.volume.from.roi get.xyz.from.index grid.equal histo.2D histo.DVH histo.from.bin histo.from.roi histo.vol load.obj.data load.obj.from.dicom load.obj.from.Rdcm load.patient.from.dicom load.patient.from.Rdcm load.Rdcm.raw.data load.T.MAT mesh.from.bin mesh.in.new.ref mesh.repair mesh.spheric.proj nesting.bin nesting.cube nesting.roi obj.create orientation.create pal.rainbow pal.RVV Rdcm.inventory Rdcm.upgrade ref.add ref.cutplane.add ref.remove ref.srctodest.add rt.chi.index rt.gamma.index rt.indices.from.bin rt.indices.from.roi save.T.MAT save.to.Rdcm select.names set.reference.obj sp.similarity.from.bin sp.similarity.from.mesh struct.clustering struct.create struct.from.bin struct.from.mesh struct.in.new.ref struct.merge struct.update_roiinfo study.deployment toy.dicom.raw toy.load.patient vector.product vol.abserror vol.copy vol.create vol.error vol.from.bin vol.gradient vol.in.new.ref vol.median vol.oversampling vol.regrid vol.repair vol.subsampling vol.sum xlsx.from.dcm xlsx.from.Rdcm

Dependencies:base64enc bslib cachem cli colorspace commonmark cpp11 crayon crosstalk curl digest DT evaluate fastmap fontawesome fs glue highr hms htmltools htmlwidgets httpuv igraph jquerylib js jsonlite knitr later lattice lazyeval lifecycle magrittr Matrix memoise mime misc3d openxlsx otel pkgconfig prettyunits progress promises qs2 R6 rappdirs rbibutils Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack rgl rlang rmarkdown Rvcg sass shiny shinyWidgets sodium sourcetools stringfish stringi tinytex V8 vctrs withr xfun xtable yaml zip

espadon overview

Rendered fromespadon_overview.Rmdusingknitr::rmarkdown

Last update: 2025-04-11
Started: 2022-06-22

Citation

Readme and manuals

Help Manual

Help page	Topics
Adding or removing a margin to a volume	add.margin
Adding shape to a 3D volume.	add.shape
Binary volume closing	bin.closing
Binary volume clustering	bin.clustering
Create a volume containing predefined shapes	bin.cuboid bin.cylinder bin.ellipsoid
Binary volume dilation	bin.dilation
Binary volume erosion	bin.erosion
Creation of a binary volume according to RoI	bin.from.roi
Creation of a binary volume according to the voxel values of a volume	bin.from.vol
Intersection of two binaries	bin.intersection
Inversion of a binary	bin.inversion
Binary volume opening	bin.opening
Subtraction of two binaries	bin.subtraction
Sum of two binaries	bin.sum
Cast of a character string	castlow.str
Cast of a character string	castup.str
DICOM raw data browser	dicom.browser
Conversion of DICOM raw data into a dataframe or a list of DICOM TAG information	dicom.parser
Anonymisation of a patient's DICOM files	dicom.patient.anonymiser
DICOM anonymizer	dicom.raw.data.anonymizer
DICOM file loading in raw data	dicom.raw.data.loader
Change TAG value in DICOM raw data	dicom.set.tag.value
DICOM TAG dictionary	dicom.tag.dictionary
DICOM TAG parser	dicom.tag.parser
Conversion of DICOM object into files that can be interpreted by the 'espadon' package	dicom.to.Rdcm.converter
DICOM content viewer	dicom.viewer
Display of a 2D histogram	display.2D.histo
Display the 3D contours of the RoI	display.3D.contour
3D display of a mesh	display.3D.mesh
Display 3D sections of a patient	display.3D.sections
Display in 3D the selected planes of an 'espadon' class volume	display.3D.stack
Display of the volume density of a histogram	display.dV_dx
Display of a DVH	display.DVH
Display of a cumulative DVH in percent of total volume	display.DVH.pc
Display of the counts of a histogram	display.histo
Display of a plane of a volume	display.kplane
Display of the RoI legend	display.legend
Display patient objects links	display.obj.links
Display of the color scale of a color palette	display.palette
Display the transverse frontal or sagittal view in the patient reference system	display.plane
Error evaluation metrics for 2-volume comparisons	err.metrics.from.bin err.metrics.from.roi
ESPADON class	espadon.class
Export espadon objects in DICOM format	export
Creation of pyramid fan object with constant angle step.	fan.beam
Creation of pyramid fan object passing through pixels of a plane.	fan.planar
Creation of spherical fan object.	fan.sphere
Indices of voxels crossed by a fan	fan.to.voxel
Coordinates of the extreme points	get.extreme.pt
Conversion of the indices of a point into ijk vector	get.ijk.from.index
Indices relating to the coordinates of the points	get.ijk.from.xyz
Image value along an axis	get.line
List of connections between objects	get.obj.connection
Extracting a plane from a volume	get.plane
Transfer matrix between two frames of reference	get.rigid.M
List of inter-connections between RoI	get.roi.connection
Value of the volume at a selection of DICOM indices	get.value.from.ijk
Voxel value at a given depth of a mesh	get.value.from.mesh
Voxel values on a selection of points	get.value.from.xyz
Volume selected by binary volume	get.volume.from.bin
Volume of a region of interest (RoI)	get.volume.from.roi
Conversion of the indices of a point, into xyz coordinate vector in the patient's frame of reference	get.xyz.from.index
Comparison of the grids of two volume objects	grid.equal
2D histograms of 2 volumes	histo.2D
Cumulative Dose Volume Histogram	histo.DVH
Histogram according to a binary	histo.from.bin
Histogram according to a RoI	histo.from.roi
Histogram of a volume	histo.vol
Load data of an 'espadon' class object	load.obj.data
Loading an 'espadon' object from DICOM files or folder	load.obj.from.dicom
Loading an 'espadon' object from *.Rdcm file	load.obj.from.Rdcm
Loading patient data from DICOM files	load.patient.from.dicom
Loading patient data from *.Rdcm files	load.patient.from.Rdcm
Loading a *.Rdcm file	load.Rdcm.raw.data
Loading of information about transfer matrices between frames of reference of patient Rdcm objects.	load.T.MAT
Creation of a mesh according to a binary volume	mesh.from.bin
Change of frame of reference of a mesh	mesh.in.new.ref
Repair of a mesh	mesh.repair
Adding spherical coordinates to a mesh	mesh.spheric.proj
Restrict volume to a binary selection	nesting.bin
Restriction of a volume to a rectangular parallelepiped	nesting.cube
Restrict volume to RoI	nesting.roi
Espadon object creating	obj.create
Creation of orientation	orientation.create
Rainbow palette	pal.rainbow
Conversion of Hounsfied Units to Realistic Volume Vizualization colors	pal.RVV
plot a 2D cut of a 3D object	plot plot.mesh plot.struct plot.volume
Inventory of 'espadon' objects from Rdcm files	Rdcm.inventory
Updating Rdcm files.	Rdcm.upgrade
Adding a frame of reference in T.MAT	ref.add
Adding volume's cutting planes frame of reference in T.MAT	ref.cutplane.add
Deletion of a frame of reference in T.MAT	ref.remove
Linking two existing frames of reference in T.MAT	ref.srctodest.add
Chi index 2D - 3D	rt.chi.index
Gamma index 2D - 3D	rt.gamma.index
Dosimetry, volume, conformity, homogeneity indices from binary selection	rt.indices.from.bin
Dosimetry, volume, conformity, homogeneity indices from RoI	rt.indices.from.roi
Save a T.MAT class object	save.T.MAT
Save a 'espadon' object in a pre-formatted *.Rdcm file	save.to.Rdcm
Regions of Interest (RoI) indices	select.names
Set the reference objects of a espadon object	set.reference.obj
Volume-based spatial similarity metrics calculated from binary modality 3D volumes.	sp.similarity.from.bin
Distance-based spatial similarity metrics calculated from the mesh.	sp.similarity.from.mesh
Clustering volumes by RoI	struct.clustering
Struct creating from contours list	struct.create
Creation of struct class object from a binary volume	struct.from.bin
Creation of struct class object from an espadon mesh	struct.from.mesh
Change of frame of reference of a "struct" class object.	struct.in.new.ref
Merging of structures into a new structure	struct.merge
Update roi.info	struct.update_roiinfo
Deployment of DICOM files from multiple patients	study.deployment
toy DICOM raw data	toy.dicom.raw
Load a toy patient for test	toy.load.patient
Vector product of two vectors	vector.product
Absolute error volume	vol.abserror
Creating a volume from another one	vol.copy
Volume creating	vol.create
Error volume	vol.error
Volume class object according to binary selection	vol.from.bin
Gradient of a volume	vol.gradient
Change of frame of reference of a volume	vol.in.new.ref
Median filter on a volume	vol.median
Oversampling a volume	vol.oversampling
Transform the grid of a volume class object into the grid of another	vol.regrid
repairing missing planes of volumes	vol.repair
Subsampling a volume	vol.subsampling
Sum of 2 volumes	vol.sum
Converting DICOM files to .xlsx files	xlsx.from.dcm
Converting .Rdcm files to .xlsx files	xlsx.from.Rdcm

Package: espadon 1.11.5

espadon: Easy Study of Patient DICOM Data in Oncology

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)