Easy Study of Patient DICOM Data in Oncology

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Documentation for package ‘espadon’ version 1.7.0

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-- A --

add.margin Adding or removing a margin to a volume

-- B --

bin.closing Binary volume closing
bin.clustering Binary volume clustering
bin.dilation Binary volume dilation
bin.erosion Binary volume erosion
bin.from.roi Creation of a binary volume according to RoI
bin.from.vol Creation of a binary volume according to the voxel values of a volume
bin.intersection Intersection of two binaries
bin.inversion Inversion of a binary
bin.opening Binary volume opening
bin.subtraction Subtraction of two binaries
bin.sum Sum of two binaries

-- C --

castlow.str Cast of a character string
castup.str Cast of a character string

-- D --

dicom.browser DICOM raw data browser
dicom.parser Conversion of DICOM raw data into a dataframe or a list of DICOM TAG information
dicom.patient.anonymiser Anonymisation of a patient's DICOM files
dicom.raw.data.anonymizer DICOM anonymizer
dicom.raw.data.loader DICOM file loading in raw data
dicom.set.tag.value Change TAG value in DICOM raw data
dicom.tag.dictionary DICOM TAG dictionary
dicom.tag.parser DICOM TAG parser
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
display.3D.contour Display the 3D contours of the RoI
display.3D.mesh 3D display of a mesh
display.3D.sections Display 3D sections of a patient
display.3D.stack Display in 3D the selected planes of an 'espadon' class volume
display.DVH Display of a DVH
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.histo Display of the counts of a histogram
display.kplane Display of a plane of a volume
display.legend Display of the RoI legend
display.obj.links Display patient objects links
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

-- E --

espadon.class ESPADON class
export Export espadon objects in dicom format

-- F --

fan.beam Creation of pyramid fan object with constant angle step.
fan.planar Creation of pyramid fan object passing through pixels of a plane.
fan.sphere Creation of spherical fan object.
fan.to.voxel Indices of voxels crossed by a fan

-- G --

get.extreme.pt Coordinates of the extreme points
get.ijk.from.index Conversion of the indices of a point into ijk vector
get.ijk.from.xyz Indices relating to the coordinates of the points
get.line Image value along an axis
get.obj.connection List of connections between objects
get.plane Extracting a plane from a volume
get.rigid.M Transfer matrix between two frames of reference
get.roi.connection List of inter-connections between RoI
get.value.from.ijk Value of the volume at a selection of DICOM indices
get.value.from.mesh Voxel value at a given depth of a mesh
get.value.from.xyz Voxel values on a selection of points
get.volume.from.bin Volume selected by binary volume
get.volume.from.roi Volume of a region of interest (RoI)
get.xyz.from.index Conversion of the indices of a point, into xyz coordinate vector in the patient's frame of reference
grid.equal Comparison of the grids of two volume objects

-- H --

histo.2D 2D histograms of 2 volumes
histo.DVH Cumulative Dose Volume Histogram
histo.from.bin Histogram according to a binary
histo.from.roi Histogram according to a RoI
histo.vol Histogram of a volume

-- L --

load.obj.data Load data of an 'espadon' class object
load.obj.from.dicom Loading an 'espadon' object from DICOM files or folder
load.obj.from.Rdcm Loading an 'espadon' object from *.Rdcm file
load.patient.from.dicom Loading patient data from DICOM files
load.patient.from.Rdcm Loading patient data from *.Rdcm files
load.Rdcm.raw.data Loading a *.Rdcm file
load.T.MAT Loading of information about transfer matrices between frames of reference of patient Rdcm objects.

-- M --

mesh.from.bin Creation of a mesh according to a binary volume
mesh.in.new.ref Change of frame of reference of a mesh
mesh.repair Repair of a mesh
mesh.spheric.proj Adding spherical coordinates to a mesh

-- N --

nesting.bin Restrict volume to a binary selection
nesting.cube Restriction of a volume to a rectangular parallelepiped
nesting.roi Restrict volume to RoI

-- O --

obj.create Espadon object creating
orientation.create Creation of orientation

-- P --

pal.rainbow Rainbow palette
pal.RVV Conversion of Hounsfied Units to Realistic Volume Vizualization colors
plot plot a 2D cut of a 3D object
plot.mesh plot a 2D cut of a 3D object
plot.struct plot a 2D cut of a 3D object
plot.volume plot a 2D cut of a 3D object

-- R --

Rdcm.inventory Inventory of 'espadon' objects from Rdcm files
Rdcm.upgrade Updating Rdcm files.
ref.add Adding a frame of reference in T.MAT
ref.cutplane.add Adding volume's cutting planes frame of reference in T.MAT
ref.remove Deletion of a frame of reference in T.MAT
ref.srctodest.add Linking two existing frames of reference in T.MAT
rt.chi.index Chi index 2D - 3D
rt.gamma.index Gamma index 2D - 3D
rt.indices.from.bin Dosimetry, volume, conformity, homogeneity indices from binary selection
rt.indices.from.roi Dosimetry, volume, conformity, homogeneity indices from RoI

-- S --

save.T.MAT Save a T.MAT class object
save.to.Rdcm Save a 'espadon' object in a pre-formatted *.Rdcm file
select.names Regions of Interest (RoI) indices
set.reference.obj Set the reference objects of a espadon object
sp.similarity.from.bin Volume-based spatial similarity metrics calculated from binary modality 3D volumes.
sp.similarity.from.mesh Distance-based spatial similarity metrics calculated from the mesh.
struct.clustering Clustering volumes by RoI
struct.from.bin Creation of struct class object from a binary volume
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.
struct.merge Merging of structures into a new structure
study.deployment Deployment of DICOM files from multiple patients

-- T --

toy.dicom.raw toy DICOM raw data
toy.load.patient Load a toy patient for test

-- V --

vector.product Vector product of two vectors
vol.copy Creating a volume from another one
vol.create Volume creating
vol.from.bin Volume class object according to binary selection
vol.gradient Gradient of a volume
vol.in.new.ref Change of frame of reference of a volume
vol.median Median filter on a volume
vol.oversampling Oversampling a volume
vol.regrid Transform the grid of a volume class object into the grid of another
vol.repair repairing missing planes of volumes
vol.subsampling Subsampling a volume
vol.sum Sum of 2 volumes

-- X --

xlsx.from.dcm Converting DICOM files to .xlsx files
xlsx.from.Rdcm Converting .Rdcm files to .xlsx files