Easy Study of Patient DICOM Data in Oncology
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Documentation for package ‘espadon’ version 1.7.2
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 |
-- 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 |