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maximemulder committed Sep 23, 2024
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166 changes: 134 additions & 32 deletions modules/api/docs/LorisRESTAPI.md
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Expand Up @@ -787,82 +787,184 @@ The JSON object is of the form:
## 5.0 DICOM Data
Like the imaging data, the DICOM data mostly lives in the `/candidates/$CandID/$Visit`
portion of the REST API namespace, but is defined in a separate section of this
Like the imaging data, the DICOM data mostly lives in the `/candidates/$CandID/$VisitLabel`
portion of the REST API namespace, but is defined in a separate section of this
document for clarity purposes.
### 5.1 Candidate DICOMs
```
GET /candidates/$CandID/$Visit/dicoms
GET /candidates/$CandID/$VisitLabel/dicoms
```
A GET request to `/candidates/$CandID/$Visit/dicoms` will return a JSON object of
all the raw DICOM data which have been acquired for that visit. It will return an
object of the form:
A GET request to `/candidates/$CandID/$VisitLabel/dicoms` will return a JSON object of
all the DICOM archives (A.K.A. one DICOM archive per `StudyInstanceUID`) which have been
acquired for that visit. It will return an object of the form:
```js
{
"Meta" : {
"CandID" : $CandID,
"Visit" : $VisitLabel,
},
"DicomTars" :
[
"DicomTars" : [
{
"Tarname" : "DCM_yyyy-mm-dd_ImagingUpload-hh-mm-abc123.tar",
"SeriesInfo" :
[{
"SeriesInfo" : [
{
"SeriesDescription" : "MPRAGE_ipat2",
"SeriesNumber" : "2",
"SeriesNumber" : 2,
"EchoTime" : "2.98",
"RepetitionTime" : "2300",
"InversionTime" : "900",
"SliceThickness" : "1",
"Modality" : "MR",
"SeriesUID" : "1.2.3.4.1107",
},
{
},
{
"SeriesDescription" : "BOLD Resting State",
"SeriesNumber" : "5",
"SeriesNumber" : 5,
"EchoTime" : "30",
"RepetitionTime" : "2100",
"InversionTime" : NULL,
"SliceThickness" : "3.5",
"Modality" : "MR",
"SeriesUID" : "3.4.5.6.1507",
}]
}
]
},
{
"Tarname" : "DCM_yyyy-mm-dd_ImagingUpload-hh-mm-def456.tar",
"SeriesInfo" :
[{
"SeriesDescription" : "MPRAGE_ipat2",
"SeriesNumber" : "2",
"EchoTime" : "2.98",
"RepetitionTime" : "2300",
"InversionTime" : "900",
"SliceThickness" : "1",
"Modality" : "MR",
"SeriesUID" : "1.7.8.9.1296",
}]
"SeriesInfo" : [
{
"SeriesDescription" : "MPRAGE_ipat2",
"SeriesNumber" : 2,
"EchoTime" : "2.98",
"RepetitionTime" : "2300",
"InversionTime" : "900",
"SliceThickness" : "1",
"Modality" : "MR",
"SeriesUID" : "1.7.8.9.1296",
}
]
}
]
]
}
```
The `Modality` header in the SeriesInfo is either `MR` or `PT` for MRI or PET
The `Modality` header in the SeriesInfo is either `MR` or `PT` for MRI or PET
scans, respectively.
```
POST /candidates/$CandID/$VisitLabel/dicoms
```
The body of the POST request should be encoded as a form data and contain a
field `File` with the imaging file, and `Json`, with the following keys and
values:
```js
{
"CandID": $CandID,
"PSCID": $PSCID,
"VisitLabel": $VisitLabel,
"IsPhantom": boolean
}
```
An optionnal header 'LORIS-Overwrite' with the value 'overwrite' can be used to
overwrite an existing file.
A successful request will be answered by a `303 See Other` response with its
`Location` header pointing to the processes list of the new upload.
(See 5.3 Tar Level processes)
### 5.2 Tar Level Data
This section describe how to upload DICOM studies and how to start and monitor
`mri_upload` processes.
DICOM studies that have been successfully uploaded and processed can be downloaded with
the following `GET` request:
```
GET /candidates/$CandID/$VisitLabel/dicoms/$Tarname
GET /candidates/$CandID/$VisitLabel/dicoms/$ArchiveName
```
Returns/Downloads a `tar` file which contains a `.meta` and a `.log` text
Returns/Downloads a `tar` file which contains a `.meta` and a `.log` text
files, and a `.tar.gz` of the raw DICOM data as acquired during the candidate
scanning session, and as retrieved from `/candidates/$CandID/$Visit/dicoms`.
scanning session, and as retrieved from `/candidates/$CandID/$VisitLabel/dicoms`.
Only `GET` is currently supported.
To get a list of the processes and their status for a given DICOM study previously uploaded use the following:
```
GET /candidates/$CandID/$VisitLabel/dicoms/$TarName/processes
```
The response contains all `mri_upload` attempts with the specified `$tarname`. And for
each of them, a list of processes status.
Response shape:
```js
{
"MriUploads": [
{
"MriUploadID": 123,
"Processes": [
{
"END_TIME": "YYYY-MM-DD hh:mm:ss",
"EXIT_CODE": "0",
"ID": "1",
"PID": "24971",
"PROGRESS": "text"
"STATE": "SUCCESS|RUNNING|ERROR"
},
...
]
},
...
]
}
```
** An empty `Processes` array means that there has never been a process launched on
that MRI upload.
To start an MRI upload process on a previously uploaded DICOM study, a POST request
containing the `MriUploadID` attribute in the request body should be sent.
```
POST /candidates/$CandID/$VisitLabel/dicoms/$TarName/processes
```
The request body must contain:
```js
{
"ProcessType": "mri_upload",
"MriUploadID": 123
}
```
Expected response: 202 Accepted with `Location` header pointing to the new process.
To obtain a specific process state, use the following:
```
GET /candidates/$CandID/$VisitLabel/dicoms/$TarName/processes/$ProcessID
```
Response shape:
```js
{
"ProcessState": [
{
"END_TIME": "YYYY-MM-DD hh:mm:ss",
"EXIT_CODE": "0",
"ID": "1",
"PID": "24971",
"PROGRESS": "text",
"STATE": "SUCCESS|RUNNING|ERROR"
}
]
}
```
## 6.0 Electrophysiology Recording Data
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