Package: tractor.base 3.4.2
Jon Clayden
tractor.base: Read, Manipulate and Visualise Magnetic Resonance Images
Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.
Authors:
tractor.base_3.4.2.tar.gz
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tractor.base.pdf |tractor.base.html✨
tractor.base/json (API)
| # Install 'tractor.base' in R: |
| install.packages('tractor.base', repos = c('https://tractor.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tractor/tractor/issues
brain-imaginggraph-algorithmsparcellationtractography
Last updated 3 months agofrom:81e9c7f1f0. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | NOTE | Sep 13 2024 |
| R-4.5-linux | NOTE | Sep 13 2024 |
| R-4.4-win | OK | Sep 13 2024 |
| R-4.4-mac | OK | Sep 13 2024 |
| R-4.3-win | OK | Sep 13 2024 |
| R-4.3-mac | OK | Sep 13 2024 |
Exports:allEqualangleBetweenVectorsasMriImageaugmentedInfoPanelcopyImageFilescreateContactSheetGraphiccreateNeighbourhoodInfocreateProjectionGraphiccreateSliceGraphicdeduplicatedeserialiseReferenceObjectembraceemptyMatrixensureFileSuffixequivalentexecuteexpandFileNameextractMriImagefifxfxyfxyzgetColourScaleidentifyImageFileNamesimageFileExistsimplodeindexListis.emptyMatrixis.nilObjectisDeserialisablelocateExecutablematchPathsmergeMriImagesnewSparseArrayWithDatanilObjectpluralisepolarPlotPanelprintLabelledValuespromotereadDicomDirectoryreadDicomFilereadImageFileregisterDeserialiserregisterPathHandlerrelativePathremoveImageFilesreorderMriImageresolvePathresolveVectorserialiseReferenceObjectsortDicomDirectoriessymlinkImageFilesthreadSafeTempFiletrimMriImagevectorCrossProductvectorLengthviewImageswherewriteImageFile
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Indexing methods | [,MriImage,ANY,ANY-method [,MriImage,ANY,missing-method [,MriImage,missing,ANY-method [,MriImage,missing,missing-method [,MriImage,MriImage,missing-method [,SparseArray,ANY,ANY-method [<-,MriImage,ANY,ANY-method [<-,MriImage,ANY,missing-method [<-,MriImage,missing,ANY-method [<-,MriImage,missing,missing-method [<-,MriImage,MriImage,missing-method [<-,SparseArray,ANY,ANY-method |
| Test whether all elements of a vector are equal | allEqual |
| Creating MriImage objects from data | asMriImage extractMriImage reorderMriImage trimMriImage |
| A simple interactive viewer for MriImage objects | augmentedInfoPanel polarPlotPanel viewImages |
| Image neighbourhoods | createNeighbourhoodInfo neighbourhoodInfo |
| Visualise MriImage objects | createContactSheetGraphic createProjectionGraphic createSliceGraphic visualisation |
| Concatenate and deduplicate vectors | deduplicate |
| The DicomMetadata class | DicomMetadata DicomMetadata-class |
| Combine similar strings into one | embrace |
| The empty matrix | emptyMatrix is.emptyMatrix |
| Test two numeric vectors for equivalence | equivalent |
| Shorthand anonymous functions | fi fx fxy fxyz |
| Obtaining colour scales | getColourScale |
| Working with MRI images stored in various formats | copyImageFiles identifyImageFileNames imageFileExists readImageFile removeImageFiles symlinkImageFiles writeImageFile |
| Create a character string by concatenating the elements of a vector | implode |
| Extract one or more elements from a list | indexList |
| Resolve a variable to a default when NULL | %||% infix |
| Reference object serialisation and deserialisation | deserialiseReferenceObject isDeserialisable registerDeserialiser serialisation serialiseReferenceObject |
| Find or run an external executable file | execute locateExecutable |
| Merging MriImage objects | mergeMriImages |
| The MriImage class | MriImage MriImage-class |
| Create a SparseArray object | newSparseArrayWithData |
| The nil object | is.nilObject nilObject |
| Number agreement with a vector | pluralise |
| Pretty print labelled information | printLabelledValues |
| Promote a vector to a single-column or single-row matrix | promote |
| Read a directory of DICOM files | readDicomDirectory |
| Read a DICOM file into a DicomMetadata object | readDicomFile |
| Functions for file name and path manipulation | ensureFileSuffix expandFileName matchPaths paths registerPathHandler relativePath resolvePath |
| Miscellaneous vector functions | angleBetweenVectors resolveVector vectorCrossProduct vectorLength |
| The SerialisableObject class | SerialisableObject SerialisableObject-class |
| Sort a directory of DICOM files into series | sortDicomDirectories |
| The SparseArray class | SparseArray SparseArray-class |
| Obtain thread-safe temporary file names | threadSafeTempFile |
| The TractorObject class | TractorObject TractorObject-class |
| Compact conditional values | where |
