HelloWord Test error

After activating InnerEye env, trying to run python InnerEye/ML/runner.py --model=HelloWorld i get this error. Ps. I am following documentation step by step

(**InnerEye) sahand@sahand-System-Product-Name:~/InnerEye-DeepLearning$ export PYTHONPATH=`pwd`
(InnerEye) sahand@sahand-System-Product-Name:~/InnerEye-DeepLearning$ python InnerEye/ML/runner.py --model=HelloWorld
Setting up logging to stdout.
Setting logging level to 20
2020-09-29T16:33:30Z INFO     rpdb is handling traps. To debug: identify the main runner.py process, then as root: kill -TRAP <process_id>; nc 127.0.0.1 4444
2020-09-29T16:33:30Z INFO     Found class HelloWorld in file /home/sahand/InnerEye-DeepLearning/InnerEye/ML/configs/segmentation/HelloWorld.py
2020-09-29T16:33:30Z INFO     Creating the default output folder structure.
2020-09-29T16:33:30Z INFO     Running outside of AzureML.
2020-09-29T16:33:30Z INFO     All results will be written to a subfolder of the project root folder.
2020-09-29T16:33:30Z INFO     Run outputs folder: /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld
2020-09-29T16:33:30Z INFO     Logs folder: /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld/logs
2020-09-29T16:33:30Z INFO     Creating the adjusted output folder structure.
2020-09-29T16:33:30Z INFO     Running outside of AzureML.
2020-09-29T16:33:30Z INFO     All results will be written to a subfolder of the project root folder.
2020-09-29T16:33:30Z INFO     Run outputs folder: /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld
2020-09-29T16:33:30Z INFO     Logs folder: /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld/logs
2020-09-29T16:33:30Z INFO     extra_code_directory is unset
Setting logging level to 20
Setting up logging with level 20 to file /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld/logs/stdout.txt
2020-09-29T16:33:33Z INFO     Setting multiprocessing start method to 'forkserver'
2020-09-29T16:33:33Z INFO     Model training will use the local dataset provided in /home/sahand/InnerEye-DeepLearning/Tests/ML/test_data
2020-09-29T16:33:33Z INFO     
Arguments:
	__center_size_param_value: None
	__dataset_data_frame_param_value: None
	__inference_stride_size_param_value: None
	__largest_connected_component_foreground_classes_param_value: None
	__min_l_rate_param_value: 0
	__model_category_param_value: ModelCategory.Segmentation
	__model_name_param_value: HelloWorld
	__overrides_param_value: None
	__use_gpu_param_value: False
	_architecture_param_value: UNet3D
	_class_weights_param_value: [0.02, 0.49, 0.49]
	_colours_param_value: [(130, 183, 14), (238, 127, 26)]
	_comparison_blob_storage_paths_param_value: None
	_crop_size_param_value: (64, 64, 64)
	_datasets_for_inference: None
	_datasets_for_training: None
	_feature_channels_param_value: [4]
	_file_system_config_param_value: <DeepLearningFileSystemConfig DeepLearningFileSystemConfig00010>
	_fill_holes_param_value: [True, True]
	_ground_truth_ids_display_names_param_value: ['region', 'region_1']
	_ground_truth_ids_param_value: ['region', 'region_1']
	_image_channels_param_value: ['channel1', 'channel2']
	_instance__params : {}
	_l_rate_multi_step_milestones_param_value: None
	_level_param_value: 50
	_local_dataset_param_value: /home/sahand/InnerEye-DeepLearning/Tests/ML/test_data
	_mask_id_param_value: mask
	_multiprocessing_start_method_param_value: MultiprocessingStartMethod.forkserver
	_name_param_value : HelloWorld00008
	_norm_method_param_value: PhotometricNormalizationMethod.CtWindow
	_num_dataload_workers_param_value: 0
	_num_epochs_param_value: 2
	_param_watchers   : {}
	_save_start_epoch_param_value: 1
	_save_step_epochs_param_value: 1
	_slice_exclusion_rules_param_value: []
	_start_epoch_param_value: 0
	_summed_probability_rules_param_value: []
	_tail_param_value : None
	_test_crop_size_param_value: (64, 64, 64)
	_test_diff_epochs_param_value: 1
	_test_start_epoch_param_value: 2
	_test_step_epochs_param_value: 1
	_train_batch_size_param_value: 2
	_use_mixed_precision_param_value: True
	_window_param_value: 200
	initialized       : True
	param             : <param.parameterized.Parameters object at 0x7f3a5dc57b00>

2020-09-29T16:33:33Z INFO     
2020-09-29T16:33:33Z INFO     **** STARTING: Model training **********************************************************************
2020-09-29T16:33:33Z INFO     
2020-09-29T16:33:33Z INFO     Train: 3, Test: 1, and Val: 2. Total subjects: 6
2020-09-29T16:33:33Z INFO     Model Training: Random seed set to: 42
2020-09-29T16:33:33Z INFO     Starting to read and parse the datasets.
2020-09-29T16:33:33Z INFO     Processing dataset (name=None)
2020-09-29T16:33:33Z INFO     Processing dataset (name=None)
2020-09-29T16:33:33Z INFO     Creating the data loader for the training set.
2020-09-29T16:33:33Z INFO     Creating the data loader for the validation set.
2020-09-29T16:33:33Z INFO     Finished creating the data loaders.
2020-09-29T16:33:33Z INFO     Models are saved at /home/sahand/InnerEye-DeepLearning/outputs/2020-09-29T163330Z_HelloWorld/checkpoints
2020-09-29T16:33:33Z INFO     Writing model summary to: logs/model_summaries/model_log001.txt
Attempted to log scalar metric LoggingColumns.NumTrainableParameters:
506139
2020-09-29T16:33:33Z INFO     Making no adjustments to the model because no GPU was found.
2020-09-29T16:33:33Z INFO     Starting training
2020-09-29T16:33:33Z INFO     Starting epoch 1
2020-09-29T16:33:33Z ERROR    Model training/testing failed. Exception: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:
sitk::ERROR: Unable to determine ImageIO reader for "/home/sahand/InnerEye-DeepLearning/Tests/ML/test_data/train_and_test_data/id1_channel1.nii.gz"
Traceback (most recent call last):
  File "InnerEye/ML/runner.py", line 364, in run_in_situ
    self.create_ml_runner().run()
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/run_ml.py", line 308, in run
    model_train(self.model_config, run_recovery)
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/model_training.py", line 150, in model_train
    train_epoch_results = train_or_validate_epoch(training_steps)
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/model_training.py", line 267, in train_or_validate_epoch
    for batch_index, sample in enumerate(train_val_params.data_loader):
  File "/home/sahand/anaconda3/envs/InnerEye/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 363, in __next__
    data = self._next_data()
  File "/home/sahand/anaconda3/envs/InnerEye/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 403, in _next_data
    data = self._dataset_fetcher.fetch(index)  # may raise StopIteration
  File "/home/sahand/anaconda3/envs/InnerEye/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/sahand/anaconda3/envs/InnerEye/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/dataset/cropping_dataset.py", line 38, in __getitem__
    sample=super().get_samples_at_index(index=i)[0],
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/dataset/full_image_dataset.py", line 289, in get_samples_at_index
    samples = [io_util.load_images_from_dataset_source(dataset_source=ds)]  # type: ignore
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/utils/io_util.py", line 357, in load_images_from_dataset_source
    images = [load_nifti_image(channel, ImageDataType.IMAGE.value) for channel in dataset_source.image_channels]
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/utils/io_util.py", line 357, in <listcomp>
    images = [load_nifti_image(channel, ImageDataType.IMAGE.value) for channel in dataset_source.image_channels]
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/utils/io_util.py", line 182, in load_nifti_image
    img, header = read_image_as_array_with_header(path)
  File "/home/sahand/InnerEye-DeepLearning/InnerEye/ML/utils/io_util.py", line 146, in read_image_as_array_with_header
    image: sitk.Image = sitk.ReadImage(str(file_path))
  File "/home/sahand/anaconda3/envs/InnerEye/lib/python3.7/site-packages/SimpleITK/SimpleITK.py", line 8876, in ReadImage
    return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:107:
sitk::ERROR: Unable to determine ImageIO reader for "/home/sahand/InnerEye-DeepLearning/Tests/ML/test_data/train_and_test_data/id1_channel1.nii.gz"

```**

[sahand68]

Hey! you got it man! thank you so much, somehow I had missed that! my bad!

[ant0nsc]

Thanks a lot @MaherJendoubi for helping @sahand68 resolve this 😃 Closing this issue now.