Importing Landmark (mrk.json) files

[amygutierrez]

I am trying to import a landmarks file that contains coordinates of 3 points. This file is a mrk.json file that is exported from 3DSlicer. I am trying to make these landmarks files import similarly to how segmentation files are also imported. My directory looks like this:
where final contains segmentation files and landmarks has the landmarks mrk.json files.

D:\DATA
└───labels
    ├───final
    ├───landmarks
    └───original

The segmentation import works well, and I have used the same process with the landmarks file:
https://github.com/amygutierrez/MONAILabel/blob/df6032d7b30b8b85ff13abb443b47c33047bfb5a/plugins/slicer/MONAILabelReviewer/MONAILabelReviewer.py#L1718-L1726

I have also changes the corresponding code in ImageDataController and MONAIServerREST.

ImageDataController.py

    def requestPointList(self, image_id: str, tag: str) -> requests.models.Response:
        print(image_id)
        print(tag)
        img_blob = self.monaiServerREST.requestPointList(image_id, tag)
        print(img_blob)
        logging.info(
            "{}: Segmentation successfully requested from MONAIServer (image id: {})".format(
                self.getCurrentTime(), image_id
            )
        )
        return img_blob

MonaiServerREST.py

    def requestPointList(self, image_id: str, tag: str) -> requests.models.Response:
        # if tag == "":
        print(tag)
        #tag = "landmarks"
        download_uri = f"{self.serverUrl}/datastore/label?label={quote_plus(image_id)}&tag={quote_plus(tag)}"
        print(f'point list download_uri: {download_uri}')
        logging.info(f"{self.getCurrentTime()}: REST: request segmentation '{download_uri}'")


        try:
            print(f'trying pointlist request')
            response = requests.get(download_uri, timeout=5)
            print(f'pointlist response: {response}')
        except Exception as exception:
            logging.warning(
                "{}: Segmentation request (image id: '{}') failed due to '{}'".format(
                    self.getCurrentTime(), image_id, exception
                )
            )
            return None
        if response.status_code != 200:
            logging.warn(
                "{}: Segmentation request (image id: '{}') failed due to response code: '{}'".format(
                    self.getCurrentTime(), image_id, response.status_code
                )
            )
            return None


        return response

I also added the appropriate file extension in data/local.py:
datasource/local.py

        extensions=("*.nii.gz", "*.nii", "*.mrk.json", "*.mrk", "*.json"),

The download_uri for the landmarks file ends up looking like this:
The file name is123456_OSTIUM.mrk.json

http://localhost:8080/datastore/label?label=123456_OSTIUM&tag=landmarks

For reference, the segmentation download_uri looks like this:
The file name is 123456_0000.nii.gz

http://localhost:8080/datastore/label?label=123456_0000&tag=final

The issue I'm experiencing is that the response I get from the request, I get a response of 404. In other words, this comes out as None
requests.get(download_uri, timeout=5)

My suspicion is that the download_uri is not pointing at the correct location, or it is not configured correctly. Would appreciate any advice on what I am doing wrong.
Thank you!!

[diazandr3s]

Hi @amygutierrez,

Thanks for opening this discussion.
How are you planning to use MONAI Label Reviewer? Did you mean the MONAI Label plugin?

Please let us know,

[amygutierrez]

Hello,
Thanks for taking the time and looking into this! Yes, I am using the slicer plugin code. But all the changes I've made are mainly the MONAILabelReviewer.py script, for our specific use case.
Basically when I import the module into 3D Slicer, the path I am using is /MONAILabel/plugins/slicer/MONAILabelReviewer and then I use the MONAILabel Reviewer module for segmentation annotation.

[diazandr3s]

Hi,

Is there a reason to use MONAILabelReviewer instead of MONAILabel plugin only?