nu_plugin_dcm 0.1.0

A nushell plugin to parse Dicom files
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# nu_plugin_dcm

A [nushell](https://www.nushell.sh/) plugin to parse [Dicom](https://en.wikipedia.org/wiki/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](https://github.com/realcundo/nu_plugin_dcm/discussions) or report problems in [Issues](https://github.com/realcundo/nu_plugin_dcm/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`.


## Examples

### Output Dicom file as a table
```sh
echo file.dcm | dcm                # uses filename/string to specify which file to open
open file.dcm | dcm                # pass binary data to `dcm`
ls I4 | dcm name                   # use `name` column as the filename
echo file.dcm | wrap foo | dcm foo # use `foo` column as the filename
open I4 | wrap foo | dcm foo       # use `foo` column as binary data
```

### Dump Dicom file as a JSON/YAML document
```sh
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
```sh
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.
```sh
let files = (ls | where type == File)

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

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

echo $files | select name size | merge { echo $files | get name | dcm | 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 to `???`.
```sh
find . -type f | lines | dcm | default Modality '???' | histogram Modality
```


## Installation

Build and install the plugin to your `PATH` using
```sh
cargo install nu_plugin_dcm
```