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vikashg / CustomTransform.py
Created January 19, 2022 17:23
This is a code for creating a custom transform where I am reading a list of images and converting to a single image
import monai
import inspect
from monai.transforms import LoadImage, AddChannel, Compose
import json
from typing import Dict, List, Optional, Sequence, Union
from monai.transforms import Transform
from monai.data.image_reader import ImageReader, ITKReader, NibabelReader, NumpyReader, PILReader
import logging
import warnings
from monai.config import DtypeLike, PathLike
@vikashg
vikashg / model_def.py
Last active August 4, 2023 16:09
This gist shows an implementation of pythonic downloading and usage of model zoo monai bundles. I propose to use the .json config files along with the ConfigParser. This model_def.py can be made more general and will be middle layer between the model_zoo and the python interface.
import torch
from monai.bundle.scripts import download
from monai.bundle.config_parser import ConfigParser
import os
class ModelDef():
def __init__(self, model_name):
download(name=model_name)
download_dir = "/home/gupta/.cache/torch/hub/bundle/" + model_name
@vikashg
vikashg / train.py
Last active September 19, 2023 13:55
A gist for debugging GeneralizeDiceScore
import logging
import os
from monai.metrics import DiceMetric, GeneralizedDiceScore
from monai.losses import GeneralizedDiceFocalLoss
import json
import sys
from monai.visualize import plot_2d_or_3d_image
import tempfile
from glob import glob
from torch.utils.tensorboard import SummaryWriter
import logging
import os
from monai.metrics import DiceMetric, GeneralizedDiceScore
from monai.losses import GeneralizedDiceFocalLoss
import json
import sys
from monai.visualize import plot_2d_or_3d_image
import tempfile
from glob import glob
from torch.utils.tensorboard import SummaryWriter