nu_plugin_dcm

A nushell plugin to parse DICOM objects.

Compatibility Matrix

Also note that this version is not fully compatible with 0.2.x and earlier versions of this plugin. The main difference is that ls *.dcm | dcm name doesn't work anymore. Use ls *.dcm | dcm, ls *.dcm | get name or ls *.dcm | select name type | dcm instead. dcm name is now reserved for the future to select dicom tags.

This plugin is in the early stage of the development. It is usable, but it might not be able to cope with all DICOM objects or DICOMweb records. See Known limitations for details.

I'm still trying to figure out what is the most useful way of using this plugin. Please feel free to try it out, send feedback in Discussions or report problems in Issues.

Usage

dcm plugin reads its input from single values or from list of values:

• dcm: expects a string/filename, file record (must contain name and type), DICOMweb record, or binary DICOM data
  • ls *.dcm | dcm: process a list of files, resulting in a list of dicom records
  • ls *.dcm | select name type | dcm: process a list of files specified by their filename, resulting in a list of dicom records
  • open --raw file.dcm | into binary | dcm: process a binary stream, resulting in a dicom record
  • open dicomweb.json | dcm: process a dicomweb record, resulting in a dicom record

See Examples for more details.

Error handling

dcm plugin works in two modes:

• default, when errors are reported as error rows, reported by nu,
• when --error option is used, errors are reported in provided column. If there were no errors, the column value is empty.

Known Limitations

• DICOM objects without a preamble and DCIM header will fail to load.

• PixelData is always skipped. For now I'm considering this to be a feature that speeds up DICOM parsing.

• dcm can process binary data. You can pass it directly to dcm as open --raw file.dcm | dcm. However, when passing a list of binary streams, nushell will try to convert it to a list of strings. To work around this, use into binary, e.g.:

  [(open --raw file1.dcm | into binary), (open --raw file2.dcm | into binary)] | dcm
  

  Without into binary, dcm would see a list of strings, assuming it's a list of filenames.

• For DICOMweb inputs, only the first of "Alphabetic", "Ideographic", "Phonetic" Patient Names is extracted.

• For DICOMweb inputs, BulkDataURI and InlineBinary are not extracted and nothing is returned as their values.

Examples

Output DICOM file as a record/table (list of records)

echo file.dcm | dcm                      # uses filename/string to specify which file to open
"file.dcm" | dcm                         # same asa above, uses filename/string to specify which file to open
open --raw file.dcm | dcm                # pass (hopefully) binary data to `dcm`
open --raw file.dcm | into binary | dcm  # pass binary data to `dcm`
ls file.dcm | dcm                        # use file records as the filename
ls file.dcm | select name type | dcm     # use file record-like records as the filename
# ls file.dcm | select name | dcm        # fails because the record only contains `name` field.
ls file.dcm | get name | dcm             # use a list of filenames (list of strings, rather than a list of records)

Dump DICOM file as a JSON/YAML document

open -r file.dcm | dcm | to json --indent 2
open -r file.dcm | dcm | to yaml

Dump all DICOM files in the current directory to a JSON/YAML document

ls *.dcm | dcm | to json --indent 2
ls *.dcm | dcm | to yaml

Find all files in the current directory and subdirectories, parse them, and group by Modality

ls **/* |
  where type == file |
  dcm -e error |
  where error == "" |
  select --ignore-errors SOPInstanceUID Modality |
  group-by Modality

For each file in the current directory, show the filename, file size, SOP Instance UID, and Modality, and sort by SOP Instance UID

let files = (ls | where type == file)

$files |
select name size |
merge ($files |
  dcm -e error |
  select --ignore-errors SOPInstanceUID Modality error
) |
sort-by size

Note that when a file cannot be parsed, it won't have SOPInstanceUID, etc. columns. Without --ignore-errors select would fail since selected columns are missing. Another option would be using default "" SOPInstanceUID to add values for missing columns.)

For each file in all subdirectories, show filename, file size, SHA256 hash of the file, SOP Instance UID, and a DICOM parsing error, if any

Use par-each to process files in parallel:

ls **/* | where type == file |
  par-each { |it| {
    name: $it.name,
    size: $it.size,
    sha256: (open --raw $it.name | hash sha256),
    dcm: ($it.name | dcm -e error)
   } } |
   select --ignore-errors name size sha256 dcm.Modality dcm.SOPInstanceUID dcm.error |
   sort-by name

Installation

Build and install using cargo:

cargo install nu_plugin_dcm

and then register in nu, e.g.

plugin add ~/.cargo/bin/nu_plugin_dcm

To start using it without restarting nu, you can import it:

plugin use ~/.cargo/bin/nu_plugin_dcm