STL plugin for Orthanc

Overview

This official plugin by the ICTEAM institute of UCLouvain extends Orthanc with support for Encapsulated 3D Manufacturing Model IODs. As of release 1.0 of the plugin, this support is limited to STL files.

The plugin allows to attach STL files to existing DICOM studies and to generate a STL mesh from structure sets (i.e., DICOM RT-STRUCT) or from NIfTI binary volumes. A high-level description of these features is available as a paper.

Importantly, any creation of a STL file requires the version of Orthanc to be above or equal to 1.12.1.

For researchers: Please cite this paper.

Compilation

Official releases can be downloaded from the Orthanc homepage. As an alternative, the repository containing the source code can be accessed using Mercurial.

The procedure to compile this plugin is similar of that for the core of Orthanc. The following commands should work on most GNU/Linux distributions, provided Docker is installed:

$ mkdir Build
$ cd Build
$ ../Resources/CreateJavaScriptLibraries.sh
$ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
$ make

The compilation will produce a shared library libOrthancSTL.so that contains the STL plugin for Orthanc.

Pre-compiled Linux Standard Base (LSB) binaries are available for download.

Pre-compiled binaries for Microsoft Windows and macOS are available as well.

Furthermore, the Docker images jodogne/orthanc-plugins and orthancteam/orthanc also contain the plugin. Debian and Ubuntu packages can be found in the standalone repository https://debian.orthanc-labs.com/.

Usage using Orthanc Explorer

The plugin extends the default Orthanc Explorer Web interface with some new features.

Attach STL file

An existing STL file can be attached to an existing DICOM study by clicking on the “Attach STL model” yellow button:

../_images/attach.png

After selecting the STL file, entering a series description, and clicking on the “Import” button, Orthanc creates a new DICOM instance that embeds the STL file. Orthanc Explorer then automatically opens the parent DICOM series containing the newly created DICOM STL instance. A button entitled “STL viewer” can then be used to render the STL:

../_images/viewers.png

Note how the STL plugin provides two viewers:

Here is a screenshot of a rendering using the Online3DViewer embedded viewer:

../_images/o3dv.png

Create STL from RT-STRUCT

The plugin can also be used to create a STL model from DICOM structure sets (RT-STRUCT) that are routinely used in the context of radiotherapy and nuclear medicine. To this end, open a DICOM RT-STRUCT series using Orthanc Explorer:

../_images/rt-struct.png

As can be seen in this screenshot, an interface opens to choose the structure set of interest, as well as the resolution of the intermediate 3D bitmap that will be used to create the STL mesh. After clicking on the “Generate” button, just like if attaching an existing STL file, Orthanc Explorer will open the newly created DICOM series and will propose to open a STL viewer.

Internally, the 3D model is generated using the well-known marching cubes algorithm, as implemented by the VTK library by Kitware. Additional technical details can be found in the reference paper.

Create STL from binary NIfTI

Besides converting RT-STRUCT to STL, it is also possible to convert a NIfTI 3D binary bitmap into a STL mesh. As this use case is very specific, it must be explicitly enabled in the configuration file of Orthanc as follows:

{
  "Plugins" : [ "libOrthancSTL.so" ],
  "STL" : {
    "EnableNIfTI" : true
  }
}

If the EnableNIfTI option is present, a new button entitled “Attach NIfTI 3D model” appears if opening an existing DICOM study:

../_images/nifti.png

This dialog box can be used to upload a NIfTI volume, and to generate a 3D mesh with a specific resolution through the marching cubes algorithm.

REST API

Besides extending the Orthanc Explorer user interface, the STL plugin adds dedicated routes to the REST API of Orthanc.

DICOM-ization of STL files

The creation of a DICOM instance that embeds an existing STL file can be done using the /tools/create-dicom route in the built-in REST API of Orthanc (starting with version 1.12.1). This route can be used similarly to the DICOM-ization of PDF files, with the data URI scheme using model/stl instead of application/pdf. Here is a working example in Python 3:

import base64
import json
import requests

with open('liver.stl', 'rb') as f:
    stl = f.read()

r = requests.post('http://localhost:8042/tools/create-dicom', json.dumps({
    'Content' : 'data:model/stl;base64,%s' % base64.b64encode(stl).decode('ascii'),
    'Parent' : '6ed7e8a4-60deff42-5e22a424-2128629f-158d0b3a',
    'Tags' : {
        'SeriesDescription' : 'Liver'
    }
}))

r.raise_for_status()
instanceId = r.json() ['ID']

Note that if the Parent field is not provided, a new DICOM study will be created.

Extraction of STL from DICOM

The route /instances/{id}/stl can be used to extract a STL from a DICOM instance embedding a STL file, where id is the Orthanc identifier of the DICOM instance. For instance:

$ curl http://localhost:8042/instances/a88c4c3f-8f2bd6fd-02080bed-92ab6817-2cb3c26e/stl > /tmp/liver.stl
$ meshlab /tmp/liver.stl

Evidently, an error is generated for DICOM instances that do not embed a STL file. Note that meshlab is a well-known desktop application to display STL file.

Listing structures of a DICOM RT-STRUCT

The STL plugin provides the list of the names of the structures that are part of a DICOM RT-STRUCT instance with Orthanc identifier id at route /stl/rt-struct/{id}. For instance:

$ curl http://localhost:8042/stl/rt-struct/f0dc2345-8f627774-f66083ae-a14d781e-1187b513
[
  "Esophagus",
  "Heart",
  "Lung_L",
  "Lung_R",
  "SpinalCord"
]

Generating a STL mesh from RT-STRUCT

A DICOM RT-STRUCT instance can be converted into a DICOM STL instance using the /stl/encode-rtstruct route provided by the STL plugin. Here is a sample Python script:

import json
import requests

r = requests.post('http://localhost:8042/stl/encode-rtstruct', json.dumps({
    'Instance' : 'f0dc2345-8f627774-f66083ae-a14d781e-1187b513',  # ID of the RT-STRUCT DICOM instance
    'RoiNames' : [ 'Lung_L', 'Lung_R' ],
    'Smooth' : True,
    'Resolution' : 256
}))

r.raise_for_status()
instanceId = r.json() ['ID']

Note that contrarily to the default user interface, this route can be used to encode multiple structure sets as a single STL model.

Generating a STL mesh from NIfTI

Here is a sample Python 3 script to convert a NIfTI file as a DICOM STL instance:

import base64
import json
import requests

with open('colon.nii.gz', 'rb') as f:
    nifti = f.read()

r = requests.post('http://localhost:8042/stl/encode-nifti', json.dumps({
    'Nifti' : 'data:application/octet-stream;base64,' + base64.b64encode(nifti).decode('ascii'),
    'ParentStudy' : '6ed7e8a4-60deff42-5e22a424-2128629f-158d0b3a',
    'Smooth' : True,
    'Resolution' : 256,
}))

r.raise_for_status()
instanceId = r.json() ['ID']

Support for Nexus

Starting with release 1.1, the STL plugin provides support for the DICOM-ization of 3D models encoded using the Nexus file format (.NXS and .NXZ extensions). Nexus provides a way to publish large, textured 3D models over Internet, with adaptive rendering depending on the available network bandwidth. Nexus is notably popular for the preservation of cultural heritage.

The plugin ships the static HTML/CSS/JavaScript assets of the official Nexus Web viewer, so that it can easily be opened right from Orthanc Explorer, as depicted in the following screenshot:

../_images/nexus.png

Starting with release 1.2 of the STL plugin, the 3DHOP viewer is also available to render DICOM-ized Nexus models:

../_images/3dhop.png

Internals

Because Nexus is not endorsed by the DICOM specification, the plugin encapsulates the Nexus file using the Raw Data IOD. The Nexus file is encoded as the (0x4205,0x1001) private DICOM tag.

Configuration

As it is non-standard, support for Nexus must be explicitly enabled in the configuration file of Orthanc as follows:

{
  "Plugins" : [ "libOrthancSTL.so" ],
  "STL" : {
    "EnableNexus" : true
  }
}

REST API

The STL plugin extends the REST API with two routes that are dedicated to the handling of Nexus files:

  1. /stl/create-nexus can be used to DICOM-ize a Nexus file. This route is a wrapper around the /tools/create-dicom standard route of Orthanc. The Nexus file must be provided as a Base64 string in the Content field of the request. Here is a sample Python script:

import base64
import json
import requests

with open('/tmp/model.nxz', 'rb') as f:
    nexus = f.read()

r = requests.post('http://localhost:8042/stl/create-nexus', json.dumps({
    'Content' : base64.b64encode(nexus).decode('ascii'),
    'Parent' : '66c8e41e-ac3a9029-0b85e42a-8195ee0a-92c2e62e',
    'Tags' : {
        'SeriesDescription' : 'Nexus',

        # Some additional tags to make the DICOM file compliant according to dciodvfy
        'AcquisitionContextSequence' : [],
        'InstanceNumber' : '1',
        'Laterality' : '',
        'SeriesNumber' : '1',
    }
}))

r.raise_for_status()
instanceId = r.json() ['ID']
  1. /instances/{id}/nexus provides access to a DICOM-ized Nexus file by decapsulating it from the DICOM instance whose Orthanc identifier is id. Importantly, this route supports HTTP range requests for adaptive streaming of Nexus models over Internet.