Julia interface for parsing/writing DICOM (Digital Imaging and Communications in Medicine) files
To install the package:
julia> using Pkg julia> Pkg.add("DICOM")
Load the package by
julia> using DICOM
Read a DICOM file by
julia> dcm_data = dcm_parse("path/to/dicom/file")
The data in
dcm_data is structured as a dictionary, and individual DICOM elements can be accessed by their hex tag.
For example, the hex tag of "Pixel Data" is
7FE0,0010, and it can be accessed in Julia by
dcm_data[(0x7FE0,0x0010)] or by
Multiple DICOM files in a folder can be read by
julia> dcm_data_array = dcmdir_parse("path/to/dicom/folder")
Data can be written to a DICOM file by
julia> dcm_write("path/to/output/file", dcm_data)
DICOM files should begin with a 128-bytes (which are ignored) followed by the string
If this preamble is missing, then the file can be parsed by
dcm_parse(path/to/file, preamble = false).
DICOM files use either explicit or implicit value representation (VR). For implicit files,
DICOM.jl will use a lookup table to guess the VR from the DICOM element's hex tag. For explicit files,
DICOM.jl will read the VRs from the file.
An auxiliary user-defined dictionary can be supplied to override the default lookup table
For example, the "Instance Number" - tag
(0x0020,0x0013) - is an integer (default VR = "IS"). We can read this as a float by setting the VR to "DS" by:
my_vrs = Dict( (0x0020,0x0013) => "DS" ) dcm_data = dcm_parse("path/to/dicom/file", aux_vr = my_vrs)
dcm_data[(0x0020,0x0013)] will return a float instead of an integer.
It is possible to skip an element by setting its VR to
For example, we can skip reading the Instance Number by
my_vrs = Dict( (0x0020,0x0013) => "" ) dcm_data = dcm_parse("path/to/dicom/file", aux_vr = my_vr)
dcm_data[(0x0020,0x0013)] will return an error because the key
(0x0020,0x0013) doesn't exist - it was skipped during reading.
The user-supplied VR can contain a master VR with the tag
(0x0000,0x0000) which will be used whenever
DICOM.jl is unable to guess the VR on its own. This is convenient for reading older dicom files and skipping retired elements - i.e. where the VR lookup fails - by:
my_vrs = Dict( (0x0000,0x0000) => "" ) dcm_data = dcm_parse("path/to/dicom/file", aux_vr = my_vrs)
A user-supplied VR can also be supplied during writing, e.g.:
julia> dcm_write("path/to/output/file", dcm_data, aux_vr = user_defined_vr)
user_defined_vr is a dictionary which maps the hex tag to the VR.
A dictionary of VRs can be obtained by passing
return_vr = true as an argument to
julia> (dcm_data, dcm_vr) = dcm_parse("path/to/dicom/file", return_vr = true)
dcm_vr will contain a dictionary of VRs for the elements in
5 days ago