nu_plugin_dcm

Note that this plugin works with nu 0.105. If you want to use nu 0.60, use version 0.1.8 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, from specific columns, or from list of values:

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.
ls *.dcm | select name | dcm: reads all files foun dby ls and returns a list of records.

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.

Examples

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

echo file.dcm | dcm                   # uses filename/string to specify which file to open
open --raw file.dcm | dcm             # pass binary data to `dcm`
ls file.dcm | dcm name                # use `name` column as the filename (equivalent of `ls file.dcm | select name | dcm`)
echo file.dcm | wrap foo | dcm foo    # use `foo` column as the filename
open -r file.dcm | into binary | wrap foo | dcm foo # use `foo` column as binary data (see Known Limitations for details)

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 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 == "" |
  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 name -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

nu_plugin_dcm 0.2.2