Package: espadon 1.8.0

Cathy Fontbonne

espadon: Easy Study of Patient DICOM Data in Oncology

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

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

espadon_1.8.0.tar.gz
espadon_1.8.0.tar.gz(r-4.5-noble)espadon_1.8.0.tar.gz(r-4.4-noble)
espadon_1.8.0.tgz(r-4.4-emscripten)espadon_1.8.0.tgz(r-4.3-emscripten)
espadon.pdf |espadon.html✨
espadon/json (API)

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

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

2.78 score 2 scripts 410 downloads 124 exports 72 dependencies

Last updated 1 months agofrom:5aa33fbcb7. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-linux-x86_64OKOct 27 2024

Exports:add.marginadd.shapebin.closingbin.clusteringbin.cuboidbin.cylinderbin.dilationbin.ellipsoidbin.erosionbin.from.roibin.from.volbin.intersectionbin.inversionbin.openingbin.subtractionbin.sumcastlow.strcastup.strdicom.browserdicom.parserdicom.patient.anonymiserdicom.raw.data.anonymizerdicom.raw.data.loaderdicom.set.tag.valuedicom.tag.dictionarydicom.tag.parserdicom.to.Rdcm.converterdicom.viewerdisplay.2D.histodisplay.3D.contourdisplay.3D.meshdisplay.3D.sectionsdisplay.3D.stackdisplay.dV_dxdisplay.DVHdisplay.DVH.pcdisplay.histodisplay.kplanedisplay.legenddisplay.obj.linksdisplay.palettedisplay.planeespadon.classexportfan.beamfan.planarfan.spherefan.to.voxelget.extreme.ptget.ijk.from.indexget.ijk.from.xyzget.lineget.obj.connectionget.planeget.rigid.Mget.roi.connectionget.value.from.ijkget.value.from.meshget.value.from.xyzget.volume.from.binget.volume.from.roiget.xyz.from.indexgrid.equalhisto.2Dhisto.DVHhisto.from.binhisto.from.roihisto.volload.obj.dataload.obj.from.dicomload.obj.from.Rdcmload.patient.from.dicomload.patient.from.Rdcmload.Rdcm.raw.dataload.T.MATmesh.from.binmesh.in.new.refmesh.repairmesh.spheric.projnesting.binnesting.cubenesting.roiobj.createorientation.createpal.rainbowpal.RVVRdcm.inventoryRdcm.upgraderef.addref.cutplane.addref.removeref.srctodest.addrt.chi.indexrt.gamma.indexrt.indices.from.binrt.indices.from.roisave.T.MATsave.to.Rdcmselect.namesset.reference.objsp.similarity.from.binsp.similarity.from.meshstruct.clusteringstruct.from.binstruct.from.meshstruct.in.new.refstruct.mergestudy.deploymenttoy.dicom.rawtoy.load.patientvector.productvol.copyvol.createvol.from.binvol.gradientvol.in.new.refvol.medianvol.oversamplingvol.regridvol.repairvol.subsamplingvol.sumxlsx.from.dcmxlsx.from.Rdcm

Dependencies:base64encBHbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldigestDTevaluatefastmapfontawesomefsgluehighrhmshtmltoolshtmlwidgetshttpuvigraphjquerylibjsjsonliteknitrlaterlatticelazyevallifecyclemagrittrmathjaxrMatrixmemoisemimemisc3dopenxlsxpkgconfigprettyunitsprogresspromisesqsR6RApiSerializerappdirsrbibutilsRcppRcppArmadilloRcppEigenRcppParallelRdpackrglrlangrmarkdownRvcgsassshinyshinyWidgetssodiumsourcetoolsstringfishstringitinytexV8vctrswithrxfunxtableyamlzip

espadon overview

Cathy & Jean-Marc Fontbonne

Rendered fromespadon_overview.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2024-03-08
Started: 2022-06-22

Readme and manuals

Help Manual

Help pageTopics
Adding or removing a margin to a volumeadd.margin
Adding shape to a 3D volume.add.shape
Binary volume closingbin.closing
Binary volume clusteringbin.clustering
Create a volume containing predefined shapesbin.cuboid bin.cylinder bin.ellipsoid
Binary volume dilationbin.dilation
Binary volume erosionbin.erosion
Creation of a binary volume according to RoIbin.from.roi
Creation of a binary volume according to the voxel values of a volumebin.from.vol
Intersection of two binariesbin.intersection
Inversion of a binarybin.inversion
Binary volume openingbin.opening
Subtraction of two binariesbin.subtraction
Sum of two binariesbin.sum
Cast of a character stringcastlow.str
Cast of a character stringcastup.str
DICOM raw data browserdicom.browser
Conversion of DICOM raw data into a dataframe or a list of DICOM TAG informationdicom.parser
Anonymisation of a patient's DICOM filesdicom.patient.anonymiser
DICOM anonymizerdicom.raw.data.anonymizer
DICOM file loading in raw datadicom.raw.data.loader
Change TAG value in DICOM raw datadicom.set.tag.value
DICOM TAG dictionarydicom.tag.dictionary
DICOM TAG parserdicom.tag.parser
Conversion of DICOM object into files that can be interpreted by the 'espadon' packagedicom.to.Rdcm.converter
DICOM content viewerdicom.viewer
Display of a 2D histogramdisplay.2D.histo
Display the 3D contours of the RoIdisplay.3D.contour
3D display of a meshdisplay.3D.mesh
Display 3D sections of a patientdisplay.3D.sections
Display in 3D the selected planes of an 'espadon' class volumedisplay.3D.stack
Display of the volume density of a histogramdisplay.dV_dx
Display of a DVHdisplay.DVH
Display of a cumulative DVH in percent of total volumedisplay.DVH.pc
Display of the counts of a histogramdisplay.histo
Display of a plane of a volumedisplay.kplane
Display of the RoI legenddisplay.legend
Display patient objects linksdisplay.obj.links
Display of the color scale of a color palettedisplay.palette
Display the transverse frontal or sagittal view in the patient reference systemdisplay.plane
ESPADON classespadon.class
Export espadon objects in dicom formatexport
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 fanfan.to.voxel
Coordinates of the extreme pointsget.extreme.pt
Conversion of the indices of a point into ijk vectorget.ijk.from.index
Indices relating to the coordinates of the pointsget.ijk.from.xyz
Image value along an axisget.line
List of connections between objectsget.obj.connection
Extracting a plane from a volumeget.plane
Transfer matrix between two frames of referenceget.rigid.M
List of inter-connections between RoIget.roi.connection
Value of the volume at a selection of DICOM indicesget.value.from.ijk
Voxel value at a given depth of a meshget.value.from.mesh
Voxel values on a selection of pointsget.value.from.xyz
Volume selected by binary volumeget.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 referenceget.xyz.from.index
Comparison of the grids of two volume objectsgrid.equal
2D histograms of 2 volumeshisto.2D
Cumulative Dose Volume Histogramhisto.DVH
Histogram according to a binaryhisto.from.bin
Histogram according to a RoIhisto.from.roi
Histogram of a volumehisto.vol
Load data of an 'espadon' class objectload.obj.data
Loading an 'espadon' object from DICOM files or folderload.obj.from.dicom
Loading an 'espadon' object from *.Rdcm fileload.obj.from.Rdcm
Loading patient data from DICOM filesload.patient.from.dicom
Loading patient data from *.Rdcm filesload.patient.from.Rdcm
Loading a *.Rdcm fileload.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 volumemesh.from.bin
Change of frame of reference of a meshmesh.in.new.ref
Repair of a meshmesh.repair
Adding spherical coordinates to a meshmesh.spheric.proj
Restrict volume to a binary selectionnesting.bin
Restriction of a volume to a rectangular parallelepipednesting.cube
Restrict volume to RoInesting.roi
Espadon object creatingobj.create
Creation of orientationorientation.create
Rainbow palettepal.rainbow
Conversion of Hounsfied Units to Realistic Volume Vizualization colorspal.RVV
plot a 2D cut of a 3D objectplot plot.mesh plot.struct plot.volume
Inventory of 'espadon' objects from Rdcm filesRdcm.inventory
Updating Rdcm files.Rdcm.upgrade
Adding a frame of reference in T.MATref.add
Adding volume's cutting planes frame of reference in T.MATref.cutplane.add
Deletion of a frame of reference in T.MATref.remove
Linking two existing frames of reference in T.MATref.srctodest.add
Chi index 2D - 3Drt.chi.index
Gamma index 2D - 3Drt.gamma.index
Dosimetry, volume, conformity, homogeneity indices from binary selectionrt.indices.from.bin
Dosimetry, volume, conformity, homogeneity indices from RoIrt.indices.from.roi
Save a T.MAT class objectsave.T.MAT
Save a 'espadon' object in a pre-formatted *.Rdcm filesave.to.Rdcm
Regions of Interest (RoI) indicesselect.names
Set the reference objects of a espadon objectset.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 RoIstruct.clustering
Creation of struct class object from a binary volumestruct.from.bin
Creation of struct class object from an espadon meshstruct.from.mesh
Change of frame of reference of a "struct" class object.struct.in.new.ref
Merging of structures into a new structurestruct.merge
Deployment of DICOM files from multiple patientsstudy.deployment
toy DICOM raw datatoy.dicom.raw
Load a toy patient for testtoy.load.patient
Vector product of two vectorsvector.product
Creating a volume from another onevol.copy
Volume creatingvol.create
Volume class object according to binary selectionvol.from.bin
Gradient of a volumevol.gradient
Change of frame of reference of a volumevol.in.new.ref
Median filter on a volumevol.median
Oversampling a volumevol.oversampling
Transform the grid of a volume class object into the grid of anothervol.regrid
repairing missing planes of volumesvol.repair
Subsampling a volumevol.subsampling
Sum of 2 volumesvol.sum
Converting DICOM files to .xlsx filesxlsx.from.dcm
Converting .Rdcm files to .xlsx filesxlsx.from.Rdcm