Container service: launch container on ROI Collection

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dr.ka...@gmail.com

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Nov 22, 2021, 2:33:42 PM11/22/21
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I'm trying to set up a container command that operates on the DICOM segmentation file associated with an ROI Collection object, created when a mask is exported with the OHIF plugin. When run manually, the container is run with:

docker run MY_IMAGE:TAG -p <XNAT-PROJECT-ID> </PATH/TO/DICOM-SEG.dcm>

My command.json is loaded successfully, but I'm not seeing an option to run the container in the Action Box when viewing an ROI Collection. Am I setting up my command correctly, both to:

1. get it to appear in the icr:roiCollectionData context, and
2. correctly parse the project-id and dicom segmentation file path?

I need the command to run on the "SEG_***.dcm" file, in the ROI Collection's files:

(base) SESSION [11:26:41]$ tree ASSESSORS/
ASSESSORS/
├── SEG_20211028_121740_525
│   └── SEG
│       ├── SEG_20211028_121740_525.dcm
│       └── SEG_catalog.xml

(command.json below)

Thanks for the help,
James

{
    "name": "i2c2-xnat-volume-calculator",
    "description": "Calculate and upload volume of dicom segmentation object.",
    "version": "1.0",
    "schema-version": "1.0",
    "image": "MYREGISTRY/i2c2-xnat-volume-calculator:v1.0",
    "type": "docker",
    "override-entrypoint": false,
    "command-line": "[PROJECT_ID] /segmentation/[DICOM_SEG_FILE_NAME]",
    "mounts": [
        {
            "name": "segmentation-in",
            "writable": "false",
            "path": "/segmentation"
        }
    ],
    "inputs": [
        {
            "name": "dicom-seg-file-name",
            "description": "DICOM segmentation file to process",
            "type": "string",
            "required": true,
            "replacement-key": "[DICOM_SEG_FILE_NAME]"
        },
        {
            "name": "project-id",
            "description": "Project ID to export results to",
            "type": "string",
            "required": true,
            "replacement-key": "[PROJECT_ID]",
            "command-line-flag": "-p"
        }
    ],
    "outputs": [
    ],
    "xnat": [
        {
            "name": "calculate-segmentation-volume",
            "description": "Calculates and uploads the ROI volume/s from a dicom segmentation object.",
            "contexts": ["icr:roiCollectionData"],
            "external-inputs": [
                {
                    "name": "segmentation",
                    "type": "Assessor",
                    "required": true,
                    "matcher": "'SEG' in @.resources[*].label",
                    "load-children": true
                }
            ],
            "derived-inputs": [
                {
                    "name": "session",
                    "type": "Session",
                    "derived-from-wrapper-input": "segmentation",
                    "required": true,
                    "load-children": true
                },
                {
                    "name": "project",
                    "type": "string",
                    "derived-from-wrapper-input": "session",
                    "derived-from-xnat-object-property": "project-id",
                    "provides-value-for-command-input": "project-id"
                },
                {
                    "name": "segmentation-dicom",
                    "type": "Resource",
                    "derived-from-wrapper-input": "segmentation",
                    "matcher": "@.label == 'SEG'",
                    "provides-files-for-command-mount": "dicom-in"
                },
                {
                    "name": "segmentation-dicom-file",
                    "type": "File",
                    "derived-from-wrapper-input": "segmentation-dicom"
                },
                {
                    "name": "segmentation-dicom-file-name",
                    "type": "string",
                    "derived-from-wrapper-input": "segmentation-dicom-file",
                    "derived-from-xnat-object-property": "name",
                    "provides-value-for-command-input": "dicom-seg-file-name",
                }
            ],
            "output-handlers": [
            ]
        }
    ]
}

Moore, Charlie

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Nov 22, 2021, 3:27:12 PM11/22/21
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Hi James,

I had to make a change to your command.json to get it imported in my XNAT. This line has a trailing comma that some JSON parsers won't accept:
                    "provides-value-for-command-input": "dicom-seg-file-name",


After changing that though, I could see your command on an ROI collection in my XNAT. To double check, did you do the following?
  1. From Administer > Plugin Settings > Command Configurations, have you enabled your command?
  2. After doing (1), have you enabled the command in the project that owns your ROI collection? That's done from (project report page) > Project Settings > Configure Commands.
Thanks,
Charlie

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Subject: [XNAT Discussion] Container service: launch container on ROI Collection
 

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dr.ka...@gmail.com

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Nov 22, 2021, 4:00:05 PM11/22/21
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It was step number 2, enabling the command in the project, that did it. I must have glossed over this in the documentation. Thanks for the quick response!

dr.ka...@gmail.com

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Nov 22, 2021, 5:04:30 PM11/22/21
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Is there a way to auto-launch a container on the saving of an Assessor? I can see in "project settings" -> "command automation" that the available events are on scan/session archiving. 

kel...@wustl.edu

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Nov 22, 2021, 5:11:05 PM11/22/21
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Hi James,
Yes! Assuming you are using XNAT 1.8.3 and Container Service 3.1, you can use the Event Service to automate the launching of your container. See Using the Event Service for Details and Enabling Automated Commands via the Event Service for details.

One small update to your command would be needed for this to work: 


 "external-inputs": [
                {
                    "name": "segmentation",
                    "type": "Assessor",
                    "required": true,
                    "matcher": "'SEG' in @.resources[*].label",
                    "load-children": true
                }

will need to be:

 "external-inputs": [
                {
                    "name": "assessor",
                    "type": "Assessor",
                    "required": true,
                    "matcher": "'SEG' in @.resources[*].label",
                    "load-children": true
                }


Best,
Matt

James Hawkins

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Nov 22, 2021, 6:08:08 PM11/22/21
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Worked like a charm, using the JSONPath filter (@.xsiType == "icr:roiCollectionData" && @.resources.length() > 0 && "SEG" in @.resources[*].label). Thanks again!

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