Hi,
I am trying to implement the Auto3DSeg Autorunner pipeline on a TCIA liver cancer dataset here. I succesfully loaded the dataset using the MONAI TciaDataset API call and made a datalist according to the MCD tutorial here. Problems arise when trying to run the AutoRunner locally on a few test images:
# Import libraries
from monai.data import DataLoader
from monai.transforms import (EnsureChannelFirstd,
Compose, LoadImaged, ResampleToMatchd)
from monai.apps import TciaDataset
from monai.apps.auto3dseg import AutoRunner
from monai.bundle import ConfigParser
from monai.config import print_config
import json
print_config()
# Specify the collection and segmentation type
collection, seg_type = "HCC-TACE-Seg", "SEG"
# Create a dictionary to map the labels in the segmentation to the labels in the image
label_dict = {'Liver': 0,
'Tumor': 1,
'vessels': 2,
'aorta': 3}
# Create a composed transform that loads the image and segmentation, then resamples the image to match the segmentation
transform = Compose(
[
LoadImaged(reader="PydicomReader", keys=["image", "label"], label_dict=label_dict),
EnsureChannelFirstd(keys=["image", "label"]),
ResampleToMatchd(keys="image", key_dst="label"),
]
)
# Create a dataset for the training and test data
train_dataset = TciaDataset(
root_dir="../data/train",
collection=collection,
section="training",
transform=transform,
download=True,
download_len=5,
seg_type=seg_type,
progress=True,
cache_rate=0.0,
val_frac=0.2,
)
test_dataset = TciaDataset(
root_dir="../data/test",
collection=collection,
section="test",
transform=transform,
download=True,
download_len=2,
seg_type=seg_type,
progress=True,
cache_rate=0.0,
val_frac=0.0,
)
data_list = {"training": train_dataset.datalist, "testing": test_dataset.datalist}
datalist_file = "../auto3dseg_datalist.json"
with open(datalist_file, "w") as f:
json.dump(data_list, f)
# Set the working directory
work_dir = "../data/auto3dseg"
# Create input configuration .yaml file
input_config = {
"name": "HCC-TACE-Seg",
"task": "segmentation",
"modality": "CT",
"datalist": "../auto3dseg_datalist.json",
"dataroot": work_dir,
}
config_yaml = "../auto3dseg_config.yaml"
ConfigParser.export_config_file(input_config, config_yaml)
train_param = {
"num_epochs_per_validation": 1,
"num_images_per_batch": 1,
"num_epochs": 1,
"num_warmup_epochs": 1,
"num_images_per_batch": 2,
}
# Create an AutoRunner
runner = AutoRunner(work_dir= work_dir,input=input_config, train=True, analyze=True, algos="swinunetr")
runner.set_training_params(train_param)
runner.set_num_fold(num_fold = 1)
runner.run()
The script fails to run due to a RunTimeError with the following stack trace:
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Cell In[36], line 13
11 runner.set_training_params(train_param)
12 runner.set_num_fold(num_fold = 1)
---> 13 runner.run()
File c:\Users\20191678\AppData\Local\anaconda3\envs\ITP\Lib\site-packages\monai\apps\auto3dseg\auto_runner.py:743, in AutoRunner.run(self)
739 logger.info("Running data analysis...")
740 da = DataAnalyzer(
741 self.datalist_filename, self.dataroot, output_path=self.datastats_filename, **self.analyze_params
742 )
--> 743 da.get_all_case_stats()
745 da = None # type: ignore
746 torch.cuda.empty_cache()
File c:\Users\20191678\AppData\Local\anaconda3\envs\ITP\Lib\site-packages\monai\apps\auto3dseg\data_analyzer.py:230, in DataAnalyzer.get_all_case_stats(self, key, transform_list)
228 result_bycase[DataStatsKeys.BY_CASE].extend(_[DataStatsKeys.BY_CASE])
229 else:
--> 230 result_bycase = self._get_all_case_stats(0, 1, None, key, transform_list)
232 summarizer = SegSummarizer(
233 self.image_key,
234 self.label_key,
(...)
239 histogram_only=self.histogram_only,
...
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "c:\Users\20191678\AppData\Local\anaconda3\envs\ITP\Lib\site-packages\monai\transforms\transform.py", line 171, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x000002688A1774D0>
It seems that the internal DataAnalyzer module is trying to apply a transform that is None by default. What is expected here?
NOTE: I am running Python 3.11.8 with the conda env dependencies specified in the MONAI repo.