nu_plugin_dcm

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 not skipped: each input is processed and errors are reported back to nu and they are not included in the output. This makes output potentially shorter than the input.
skip errors using -s/--silent-errors flag: errors are output as empty values. This means that the output has exactly the same number of rows as the input. This mode is suitable for merging tables (e.g. table of files and table of parsed dicom objects).

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 --pretty 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 --pretty 2
ls *.dcm | dcm name | to yaml

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. dcm is run using --silent-errors/-s to make sure that both $files and dcm have the same number of rows. Without the flag the output of dcm could be shorted if Dicom object couldn't be parsed resulting in incorrect merge.

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

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

dcm name is a shortcut for get name | dcm. The following commands are equivalent:

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

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

echo $files | select name size | merge { echo $files | get name | dcm -s | select SOPInstanceUID Modality PixelSpacing.0 PixelSpacing.1 } | sort-by size

Find all files in the current directory and subdirectories, parse them and output a histogram of modalities

Note that not all Dicom files have (0008,0060) Modality tag available. This will default missing Modality tags to ???.

find . -type f | lines | dcm | default Modality '???' | histogram Modality

Installation

Build and install in the same directory as nu command. Alternatively add the installation path to your plugin_dirs in your config.toml.

cargo install nu_plugin_dcm

Note that at the time of writing the Nu documentation is out of date and PATH env variable is NOT used to discover plugins.

nu_plugin_dcm 0.1.2