fix: dicom json launch and documentation (#2642)

* fix: typo in metadataProvider class name

* docs: Add dicom-json documentation

* fix: documentation with s3 links

extensions/default/src/DicomJSONDataSource/index.js

@@ -3,7 +3,7 @@ import OHIF from '@ohif/core';
 
 import getImageId from '../DicomWebDataSource/utils/getImageId';
 
-const metadataProvider = OHIF.classes.metadataProvider;
+const metadataProvider = OHIF.classes.MetadataProvider;
 
 const mappings = {
   studyInstanceUid: 'StudyInstanceUID',
@@ -93,7 +93,7 @@ function createDicomJSONApi(dicomJsonConfig) {
     },
     query: {
       studies: {
-        mapParams: () => { },
+        mapParams: () => {},
         search: async param => {
           const [key, value] = Object.entries(param)[0];
           const mappedParam = mappings[key];

platform/docs/docs/configuration/dataSources/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Data Sources",
+  "position": 2
+}

platform/docs/docs/configuration/dataSources/dicom-json.md

@@ -0,0 +1,155 @@
+---
+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://v3-demo.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.
+
+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).
+
+```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
+  ]
+}
+```
+
+![](../../assets/img/dicom-json.png)
+
+### Local Demo
+
+You can run OHIF with a JSON data source againts 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:
+
+![](../../assets/img/dicom-json-public.png)

platform/docs/docs/configuration/dataSources/dicom-web.md

@@ -1,9 +1,9 @@
 ---
-sidebar_position: 2
+sidebar_position: 1
-sidebar_label: Data Sources
+sidebar_label: DICOMweb
 ---
 
-# Data Sources
+# DICOMweb
 
 ## Set up a local DICOM server
 
@@ -97,7 +97,7 @@ yarn run dev:orthanc
 #### Configuration: Learn More
 
 > For more configuration fun, check out the
-> [Essentials Configuration](./index.md) guide.
+> [Essentials Configuration](../index.md) guide.
 
 Let's take a look at what's going on under the hood here. `yarn run dev:orthanc`
 is running the `dev:orthanc` script in our project's `package.json` (inside
@@ -154,7 +154,7 @@ window.config = {
 ```
 
 To learn more about how you can configure the OHIF Viewer, check out our
-[Configuration Guide](./index.md).
+[Configuration Guide](../index.md).
 
 ### Running DCM4CHEE
 
@@ -189,42 +189,3 @@ below:
   https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/html-templates
 [config-files]:
   https://github.com/OHIF/Viewers/tree/master/platform/viewer/public/config
-
-## Static Files
-
-There is a binay DICOM to static file generator, which provides easily served
-binary files.  The files are all compressed in order to reduce space signifcantly,
-and are pre-computed for the files required for OHIF, so that the performance
-of serving the files is just the read from disk/write to http stream time, without
-any extra processing time.
-
-The project for the static wado files is located here:
-[static-wado]: https://github.com/wayfarer3130/static-wado
-
-It can be compiled with Java and Gradle, and then run against a set of dicom,
-in the example located in /dicom/study1 outputting to /dicomweb, and then a
-server run against that data, like this:
-```
-git clone https://github.com/wayfarer3130/static-wado.git
-cd static-wado
-./gradlew installDist
-StaticWado/build/install/StaticWado/bin/StaticWado -d /dicomweb /dicom/study1
-cd /dicomweb
-npx http-server -p 5000 --cors -g
-```
-
-There is then a dev environment in the platform/viewer directory which can be run
-against those files, like this:
-```
-cd platform/viewer
-yarn dev:static
-```
-
-Additional studies can be added to the dicomweb by re-running the StaticWado command.
-It will create a single studies.gz index file (JSON DICOM file, compressed)
-containing an index of all studies created.  There is then a small extension
-to OHIF which performs client side indexing.
-
-The StaticWado command also knows how to deploy a client and dicomweb directory
-to Amazon s3, which can then server files up directly.  There is another
-build setup build:aws in the viewer package.json to create such a deployment.

platform/docs/docs/configuration/dataSources/static-files.md

@@ -0,0 +1,45 @@
+---
+sidebar_position: 2
+sidebar_label: Static Files
+---
+
+# Static Files
+
+There is a binary DICOM to static file generator, which provides easily served
+binary files. The files are all compressed in order to reduce space
+significantly, and are pre-computed for the files required for OHIF, so that the
+performance of serving the files is just the read from disk/write to http stream
+time, without any extra processing time.
+
+The project for the static wado files is located here: [static-wado]:
+https://github.com/wayfarer3130/static-wado
+
+It can be compiled with Java and Gradle, and then run against a set of dicom, in
+the example located in /dicom/study1 outputting to /dicomweb, and then a server
+run against that data, like this:
+
+```
+git clone https://github.com/wayfarer3130/static-wado.git
+cd static-wado
+./gradlew installDist
+StaticWado/build/install/StaticWado/bin/StaticWado -d /dicomweb /dicom/study1
+cd /dicomweb
+npx http-server -p 5000 --cors -g
+```
+
+There is then a dev environment in the platform/viewer directory which can be
+run against those files, like this:
+
+```
+cd platform/viewer
+yarn dev:static
+```
+
+Additional studies can be added to the dicomweb by re-running the StaticWado
+command. It will create a single studies.gz index file (JSON DICOM file,
+compressed) containing an index of all studies created. There is then a small
+extension to OHIF which performs client side indexing.
+
+The StaticWado command also knows how to deploy a client and dicomweb directory
+to Amazon s3, which can then server files up directly. There is another build
+setup build:aws in the viewer package.json to create such a deployment.