#nushell #dicom #nu

bin+lib nu_plugin_dcm

A nushell plugin to parse Dicom files

8 releases

Uses new Rust 2021

0.1.7 Jun 8, 2022
0.1.6 May 7, 2022
0.1.5 Apr 4, 2022
0.1.4 Mar 31, 2022
0.1.1 Jul 26, 2021

#2 in #nushell

Download history 1/week @ 2022-03-08 12/week @ 2022-03-15 12/week @ 2022-03-22 27/week @ 2022-03-29 23/week @ 2022-04-05 3/week @ 2022-04-12 44/week @ 2022-04-26 65/week @ 2022-05-03 109/week @ 2022-05-10 25/week @ 2022-05-17 42/week @ 2022-05-24 57/week @ 2022-05-31 40/week @ 2022-06-07 6/week @ 2022-06-14

147 downloads per month

MIT and maybe CC-PDDC

22KB
409 lines

nu_plugin_dcm

Note that this plugin works with nu>=0.60. If you want to use nu<=0.44, use version 0.1.3 of this plugin.

A nushell plugin to parse Dicom objects.

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. One notable limitation is that all Dicom objects are expected to have a preamble.

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 specific columns:

  • dcm: expects a string/filename or binary Dicom data
  • dcm $column_name: reads a string/filename or binary Dicom data from $column. This is equivalent to get $column | dcm.

Error handling

dcm plugin works in two modes:

  • default, when errors are reported as error rows,
  • in custom columns when --error option is used. This will report all errors in the specified column. Empty column value means no error.

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.

Examples

Output Dicom file as a table

echo file.dcm | dcm                # uses filename/string to specify which file to open
open file.dcm | dcm                # pass binary data to `dcm`
ls file.dcm | dcm name             # use `name` column as the filename
echo file.dcm | wrap foo | dcm foo # use `foo` column as the filename
open file.dcm | wrap foo | dcm foo # use `foo` column as binary data

Dump Dicom file as a JSON/YAML document

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

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

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

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

ls **/* |
  where type == file |
  dcm name -e error |
  where error == "" |
  group-by Modality

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

PixelSpacing is an array with 2 values.

To flatten the array use .0 and .1 indices.

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

echo $files |
  select name size |
  merge {
    echo $files |
    dcm name -e error |
    default "" SOPInstanceUID |
    select SOPInstanceUID Modality PixelSpacing.0 PixelSpacing.1 error
  } |
  sort-by size

Note that when a file cannot be parsed, it won't have SOPInstanceUID column. The default commands makes sure that select can find the column.

You can also use each and par-each like in the following example.

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 **/* |
  par-each { |it| {
    name: $it.name,
    size: $it.size,
    sha256: (open $it.name | hash sha256),
    dcm: ($it.name | dcm -e error)
   } } |
   select 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 via

register --encoding=json <PATH-TO-nu_plugin_dcm>/nu_plugin_dcm

Note that you must use json encoding. capnp is not supported yet.

Dependencies

~19MB
~370K SLoC