Easy Study of Patient DICOM Data in Oncology

Documentation for package ‘espadon’ version 1.10.0

Help Pages

-- A --

add.margin	Adding or removing a margin to a volume
add.shape	Adding shape to a 3D volume.

-- B --

bin.closing	Binary volume closing
bin.clustering	Binary volume clustering
bin.cuboid	Create a volume containing predefined shapes
bin.cylinder	Create a volume containing predefined shapes
bin.dilation	Binary volume dilation
bin.ellipsoid	Create a volume containing predefined shapes
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 --

err.metrics.from.roi	Error evaluation metrics for 2-volume comparisons
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.create	Struct creating from contours list
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.abserror	Absolute error volume
vol.copy	Creating a volume from another one
vol.create	Volume creating
vol.error	Error volume
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