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Read DICOM Metadata into a Tidy Tibble

Source: R/read.R
read_dicom.Rd

Reads one or more DICOM files (or directories of DICOM files) using the native C++17 / DCMTK parser and returns a tidy tibble::tibble.

Usage

read_dicom(path, wide = FALSE, include_sequences = FALSE, recursive = TRUE)

Arguments

path

Character vector of DICOM file paths or directory paths.

wide

Logical. If FALSE (default), returns long format with one row per DICOM attribute (file, tag, group, element, vr, length, vm, keyword, name, value). If TRUE, pivots to wide format with one row per file and one column per DICOM keyword.

include_sequences

Logical. If TRUE, recursively extracts nested sequence (SQ) items. Default is FALSE.

recursive

Logical. When path contains directories, search subdirectories recursively. Default is TRUE.

Value

A tibble::tibble of class c("dicom_tbl", "tbl_df", "tbl", "data.frame").

Examples

dcm_file <- system.file("extdata", "example.dcm", package = "dicomtk")
hdr <- read_dicom(dcm_file)
hdr
#> # A tibble: 190 × 12
#>    file         tag   group element vr    length vm    keyword name  value depth
#>    <chr>        <chr> <chr> <chr>   <chr>  <int> <chr> <chr>   <chr> <chr> <int>
#>  1 "C:\\Users\… (000… 0002  0000    UL         4 1     FileMe… File… "192"     0
#>  2 "C:\\Users\… (000… 0002  0001    OB         2 1     FileMe… File… "00\…     0
#>  3 "C:\\Users\… (000… 0002  0002    UI        26 1     MediaS… Medi… "1.2…     0
#>  4 "C:\\Users\… (000… 0002  0003    UI        48 1     MediaS… Medi… "1.3…     0
#>  5 "C:\\Users\… (000… 0002  0010    UI        20 1     Transf… Tran… "1.2…     0
#>  6 "C:\\Users\… (000… 0002  0012    UI        18 1     Implem… Impl… "1.3…     0
#>  7 "C:\\Users\… (000… 0002  0013    SH        10 1     Implem… Impl… "DCT…     0
#>  8 "C:\\Users\… (000… 0002  0016    AE         8 1     Source… Sour… "CLU…     0
#>  9 "C:\\Users\… (000… 0008  0005    CS        10 1-n   Specif… Spec… "ISO…     0
#> 10 "C:\\Users\… (000… 0008  0008    CS        22 2-n   ImageT… Imag… "ORI…     0
#> # ℹ 180 more rows
#> # ℹ 1 more variable: sequence_path <chr>

# Wide format (1 row per file)
read_dicom(dcm_file, wide = TRUE)
#> # A tibble: 1 × 88
#>   file      FileMetaInformationG…¹ FileMetaInformationV…² MediaStorageSOPClass…³
#>   <chr>     <chr>                  <chr>                  <chr>                 
#> 1 "C:\\Use… 192                    "00\\01"               1.2.840.10008.5.1.4.1…
#> # ℹ abbreviated names: ¹​FileMetaInformationGroupLength,
#> #   ²​FileMetaInformationVersion, ³​MediaStorageSOPClassUID
#> # ℹ 84 more variables: MediaStorageSOPInstanceUID <chr>,
#> #   TransferSyntaxUID <chr>, ImplementationClassUID <chr>,
#> #   ImplementationVersionName <chr>, SourceApplicationEntityTitle <chr>,
#> #   SpecificCharacterSet <chr>, ImageType <chr>, InstanceCreationDate <chr>,
#> #   InstanceCreationTime <chr>, InstanceCreatorUID <chr>, SOPClassUID <chr>, …