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DICOM

Julia package for reading and writing DICOM (Digital Imaging and Communications in Medicine) files

Readme

DICOM.jl

Julia interface for parsing/writing DICOM (Digital Imaging and Communications in Medicine) files

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Usage

Installation

To install the package:

julia> using Pkg
julia> Pkg.add("DICOM")

Load the package by

julia> using DICOM

Reading Data

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 dcm_data[tag"PixelData"].

Multiple DICOM files in a folder can be read by

julia> dcm_data_array = dcmdir_parse("path/to/dicom/folder")

Writing Data

Data can be written to a DICOM file by

julia> dcm_write("path/to/output/file", dcm_data)

Additional Notes

DICOM files should begin with a 128-bytes (which are ignored) followed by the string DICM. 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)
    

    Now 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)
    

    and now 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)
    

    where 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 dcm_parse(), e.g.:

    julia> (dcm_data, dcm_vr) = dcm_parse("path/to/dicom/file", return_vr = true)
    

    and dcm_vr will contain a dictionary of VRs for the elements in dcm_data

First Commit

03/01/2013

Last Touched

5 days ago

Commits

165 commits