Project-MONAI / Project-MONAI/MONAILabel

Need new scoring method to count inferred labels

Open
#1,444 2 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
891
Forks
269
Avg merge
15h 41m
Merged PRs (30d)
1

Description

Describe the solution you'd like
After running batch inference on your data (labeled and/or unlabeled ), It would be useful to find volumes where the model missed an organ / disease. Or over estimated / under estimated an organ or disease.
For example:

  • Data set is for liver tumor, where are the images without tumors? This is either the AI missed the tumor and it must be labeled or it is a true normal and the data scientiest want to exclude this normal images
  • Where are the images with 3 kidneys ? or kidney pixel count > xx pixels

This request may need to count pixels as well as calculate the actual volume in mm^3

Describe alternatives you've considered
I managed to adapt the the code from the sum scoring as

import logging
import numpy as np
import torch
from monai.transforms import LoadImage
from monailabel.interfaces.datastore import Datastore, DefaultLabelTag
from monailabel.interfaces.tasks.scoring import ScoringMethod
from monailabel.interfaces.app import MONAILabelApp
from monailabel.interfaces.utils.app import app_instance

logger = logging.getLogger(__name__)

class LabelCount(ScoringMethod):
    """
    Compute pixel count for each label
    """
    def __init__(self):
        super().__init__("Compute label count for an inference ")

    def info(self):
        instance: MONAILabelApp = app_instance()
        dataStore: Datastore = instance.datastore()
        status = dataStore.status()
        label_tag = list(status['label_tags'].keys())

        return {
            "description": self.description,
            "config":
                {"label_tag": label_tag
                 }
        }

    def __call__(self, request, datastore: Datastore):
        loader = LoadImage(image_only=True)
        tag = request.get("label_tag", "")
        if not tag:
            logger.error(" scoring error! Need to pass a label_tag")
            return {}

        result = {}
        for image_id in datastore.list_images():
            label_id: str = datastore.get_label_by_image_id(image_id, tag)
            if label_id:
                uri = datastore.get_label_uri(label_id, tag)
                # logger.info(f" ============{label_id=} ===={uri=}")
                label = loader(uri)
                if isinstance(label, torch.Tensor):
                    label = label.numpy()

                lbs,lbs_count=np.unique(label, return_counts=True)
                lbs_count_dict={}
                for i, lb in enumerate(lbs):
                    lbs_count_dict[str(int(lb))]=int(lbs_count[i])  # int conversion is needed to avoid json error
                logger.info(f"============{label_id=} ===={uri=} organs found for {image_id} are {lbs_count_dict} ")

                # datastore.update_image_info(image_id, lbs_count_dict)
                datastore.update_label_info(label_id, tag, {"label_count": lbs_count_dict})
                result[label_id] = {"label_count": lbs_count_dict}
        return result

Additional context
This needs an active learning to sort by the most or least number of pixels for each label.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading monailabel/tasks/scoring/sum.py and the ScoringMethod interface, then compare the proposed LabelCount code with the datastore methods it uses. Done should define how inferred labels are counted, whether pixel counts and volumes are supported, and how results can be sorted for active learning.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python, pytorch
Domain
data, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.