# Easy Study of Patient DICOM Data in Oncology

## Documentation for package ‘espadon’ version 1.11.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H L M N O P R S T V X

## -- 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.bin | Error evaluation metrics for 2-volume comparisons
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
struct.update_roiinfo | Update roi.info
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