195 lines
8.0 KiB
Markdown
195 lines
8.0 KiB
Markdown
|
---
|
||
|
|
sidebar_position: 3
|
||
|
|
sidebar_label: DICOM JSON
|
||
|
|
---
|
||
|
|
|
||
|
|
# DICOM JSON
|
||
|
|
|
||
|
|
You can launch the OHIF Viewer with a JSON file which points to a DICOMWeb
|
||
|
|
server as well as a list of study and series instance UIDs along with metadata.
|
||
|
|
|
||
|
|
An example would look like
|
||
|
|
|
||
|
|
`https://viewer.ohif.org/viewer/dicomjson?url=https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001.json`
|
||
|
|
|
||
|
|
As you can see the url to the location of the JSON file is passed in the query
|
||
|
|
after the `dicomjson` string, which is
|
||
|
|
`https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001.json` (this
|
||
|
|
json file has been generated by OHIF team and stored in an amazon s3 bucket for
|
||
|
|
the purpose of the guide).
|
||
|
|
|
||
|
|
## DICOM JSON sample
|
||
|
|
|
||
|
|
Here we are using the LIDC-IDRI-0001 case which is a sample of the LIDC-IDRI
|
||
|
|
dataset. Let's have a look at the JSON file:
|
||
|
|
|
||
|
|
### Metadata
|
||
|
|
|
||
|
|
JSON file stores the metadata for the study level, series level and instance
|
||
|
|
level. A JSON launch file should follow the same structure as the one below.
|
||
|
|
|
||
|
|
:::tip
|
||
|
|
You can use our script to generate the JSON file from a hosted endpoint. See
|
||
|
|
`.scripts/dicom-json-generator.js`
|
||
|
|
|
||
|
|
You could run it like this:
|
||
|
|
|
||
|
|
```bash
|
||
|
|
node .scripts/dicom-json-generator.js '/path/to/study/folder' 'url/to/dicom/server/folder' 'json/output/file.json'
|
||
|
|
```
|
||
|
|
|
||
|
|
Some modalities require additional metadata to be added to the JSON file. You can read more about the minimum amount of metadata required for the viewer to work [here](../../faq.md#what-are-the-list-of-required-metadata-for-the-ohif-viewer-to-work). We will handle this in the script. For example, the script will add the CodeSequences for SR in order to display the measurements in the viewer.
|
||
|
|
:::
|
||
|
|
|
||
|
|
|
||
|
|
Note that at the instance level metadata we are storing both the `metadata` and
|
||
|
|
also the `url` for the dicom file on the dicom server. In this case we are
|
||
|
|
referring to
|
||
|
|
`dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm`
|
||
|
|
which is stored in another directory in our s3. (You can actually try
|
||
|
|
downloading the dicom file by opening the url in your browser).
|
||
|
|
|
||
|
|
The URL to the script in the given example is `https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178`. This URL serves as the parent directory that contains all the series within their respective folders.
|
||
|
|
|
||
|
|
```json
|
||
|
|
{
|
||
|
|
"studies": [
|
||
|
|
// first study metadata
|
||
|
|
{
|
||
|
|
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
|
||
|
|
"StudyDate": "20000101",
|
||
|
|
"StudyTime": "",
|
||
|
|
"PatientName": "",
|
||
|
|
"PatientID": "LIDC-IDRI-0001",
|
||
|
|
"AccessionNumber": "",
|
||
|
|
"PatientAge": "",
|
||
|
|
"PatientSex": "",
|
||
|
|
"series": [
|
||
|
|
// first series metadata
|
||
|
|
{
|
||
|
|
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
|
||
|
|
"SeriesNumber": 3000566,
|
||
|
|
"Modality": "CT",
|
||
|
|
"SliceThickness": 2.5,
|
||
|
|
"instances": [
|
||
|
|
// first instance metadata
|
||
|
|
{
|
||
|
|
"metadata": {
|
||
|
|
"Columns": 512,
|
||
|
|
"Rows": 512,
|
||
|
|
"InstanceNumber": 1,
|
||
|
|
"SOPClassUID": "1.2.840.10008.5.1.4.1.1.2",
|
||
|
|
"PhotometricInterpretation": "MONOCHROME2",
|
||
|
|
"BitsAllocated": 16,
|
||
|
|
"BitsStored": 16,
|
||
|
|
"PixelRepresentation": 1,
|
||
|
|
"SamplesPerPixel": 1,
|
||
|
|
"PixelSpacing": [0.703125, 0.703125],
|
||
|
|
"HighBit": 15,
|
||
|
|
"ImageOrientationPatient": [1, 0, 0, 0, 1, 0],
|
||
|
|
"ImagePositionPatient": [-166, -171.699997, -10],
|
||
|
|
"FrameOfReferenceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.229925374658226729607867499499",
|
||
|
|
"ImageType": ["ORIGINAL", "PRIMARY", "AXIAL"],
|
||
|
|
"Modality": "CT",
|
||
|
|
"SOPInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.262721256650280657946440242654",
|
||
|
|
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
|
||
|
|
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
|
||
|
|
"WindowCenter": -600,
|
||
|
|
"WindowWidth": 1600,
|
||
|
|
"SeriesDate": "20000101"
|
||
|
|
},
|
||
|
|
"url": "dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm"
|
||
|
|
},
|
||
|
|
// second instance metadata
|
||
|
|
{
|
||
|
|
"metadata": {
|
||
|
|
"Columns": 512,
|
||
|
|
"Rows": 512,
|
||
|
|
"InstanceNumber": 2,
|
||
|
|
"SOPClassUID": "1.2.840.10008.5.1.4.1.1.2",
|
||
|
|
"PhotometricInterpretation": "MONOCHROME2",
|
||
|
|
"BitsAllocated": 16,
|
||
|
|
"BitsStored": 16,
|
||
|
|
"PixelRepresentation": 1,
|
||
|
|
"SamplesPerPixel": 1,
|
||
|
|
"PixelSpacing": [0.703125, 0.703125],
|
||
|
|
"HighBit": 15,
|
||
|
|
"ImageOrientationPatient": [1, 0, 0, 0, 1, 0],
|
||
|
|
"ImagePositionPatient": [-166, -171.699997, -12.5],
|
||
|
|
"FrameOfReferenceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.229925374658226729607867499499",
|
||
|
|
"ImageType": ["ORIGINAL", "PRIMARY", "AXIAL"],
|
||
|
|
"Modality": "CT",
|
||
|
|
"SOPInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.512235483218154065970649917292",
|
||
|
|
"SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
|
||
|
|
"StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
|
||
|
|
"WindowCenter": -600,
|
||
|
|
"WindowWidth": 1600,
|
||
|
|
"SeriesDate": "20000101"
|
||
|
|
},
|
||
|
|
"url": "dicomweb:https://ohif-dicom-json-example.s3.amazonaws.com/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-002.dcm"
|
||
|
|
}
|
||
|
|
// ..... other instances metadata
|
||
|
|
]
|
||
|
|
}
|
||
|
|
// ... other series metadata
|
||
|
|
],
|
||
|
|
"NumInstances": 133,
|
||
|
|
"Modalities": "CT"
|
||
|
|
}
|
||
|
|
// second study metadata
|
||
|
|
]
|
||
|
|
}
|
||
|
|
```
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
### Local Demo
|
||
|
|
|
||
|
|
You can run OHIF with a JSON data source against you local datasets (given that
|
||
|
|
their JSON metadata is extracted).
|
||
|
|
|
||
|
|
First you need to put the JSON file and the folder containing the dicom files
|
||
|
|
inside your `public` folder. Since files are served from your local server the
|
||
|
|
`url` for the JSON file will be `http://localhost:3000/LIDC-IDRI-0001.json` and
|
||
|
|
the dicom files will be
|
||
|
|
`dicomweb:http://localhost:3000/LIDC-IDRI-0001/01-01-2000-30178/3000566.000000-03192/1-001.dcm`.
|
||
|
|
|
||
|
|
After `yarn install` and running `yarn dev` and opening the browser at
|
||
|
|
`http://localhost:3000/viewer/dicomjson?url=http://localhost:3000/LIDC-IDRI-0001.json`
|
||
|
|
will display the viewer.
|
||
|
|
|
||
|
|
Download JSON file from
|
||
|
|
[here](https://www.dropbox.com/sh/zvkv6mrhpdze67x/AADLGK46WuforD2LopP99gFXa?dl=0)
|
||
|
|
|
||
|
|
Sample DICOM files can be downloaded from
|
||
|
|
[TCIA](https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI) or
|
||
|
|
directly from
|
||
|
|
[here](https://www.dropbox.com/sh/zvkv6mrhpdze67x/AADLGK46WuforD2LopP99gFXa?dl=0)
|
||
|
|
|
||
|
|
Your public folder should look like this:
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
:::tip
|
||
|
|
It is important to URL encode the `url` query parameter especially if the `url`
|
||
|
|
parameter itself also contains query parameters. So for example,
|
||
|
|
|
||
|
|
`http://localhost:3000/viewer/dicomjson?url=http://localhost:3000/LIDC-IDRI-0001.json?key0=val0&key1=val1`
|
||
|
|
|
||
|
|
should be...
|
||
|
|
|
||
|
|
`http://localhost:3000/viewer/dicomjson?url=http://localhost:3000/LIDC-IDRI-0001.json?key0=val0%26key1=val1`
|
||
|
|
|
||
|
|
Notice the ampersand (`&`) is encoded as `%26`.
|
||
|
|
:::
|
||
|
|
|
||
|
|
:::note
|
||
|
|
When hosting the DICOM JSON files, it is important to be aware that certain providers
|
||
|
|
do not automatically handle the 404 error and fallback to index.html. For example, Netlify
|
||
|
|
handles this, but Azure does not. Consequently, when you attempt to access a link with a
|
||
|
|
specific URL, a 404 error will be displayed.
|
||
|
|
|
||
|
|
This issue also occurs locally, where the http-server does not handle it. However,
|
||
|
|
if you utilize the `serve` package (npx serve ./dist -c ../public/serve.json), it effectively addresses this problem.
|
||
|
|
:::
|