Closed
Description
Describe the bug
./modules/interpretability/class_lung_lesion.ipynb
04:16:40 Running ./modules/interpretability/class_lung_lesion.ipynb
04:16:40 Checking PEP8 compliance...
04:16:40 Running notebook...
04:16:40 Before:
04:16:40 "max_epochs = 100\n",
04:16:40 After:
04:16:40 "max_epochs = 1\n",
04:16:40 Before:
04:16:40 "val_interval = 1\n",
04:16:40 After:
04:16:40 "val_interval = 1\n",
04:16:51
Executing: 0%| | 0/20 [00:00<?, ?cell/s]
Executing: 5%|▌ | 1/20 [00:01<00:28, 1.50s/cell]
Executing: 10%|█ | 2/20 [00:04<00:45, 2.51s/cell]
Executing: 15%|█▌ | 3/20 [00:07<00:41, 2.44s/cell]
Executing: 20%|██ | 4/20 [00:09<00:37, 2.37s/cell]
Executing: 45%|████▌ | 9/20 [00:09<00:07, 1.51cell/s]
Executing: 45%|████▌ | 9/20 [00:10<00:12, 1.16s/cell]
04:16:51 Traceback (most recent call last):
04:16:51 File "/opt/conda/bin/papermill", line 8, in <module>
04:16:51 sys.exit(papermill())
04:16:51 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
04:16:51 return self.main(*args, **kwargs)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1062, in main
04:16:51 rv = self.invoke(ctx)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
04:16:51 return ctx.invoke(self.callback, **ctx.params)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 763, in invoke
04:16:51 return __callback(*args, **kwargs)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
04:16:51 return f(get_current_context(), *args, **kwargs)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
04:16:51 execute_notebook(
04:16:51 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
04:16:51 raise_for_execution_errors(nb, output_path)
04:16:51 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
04:16:51 raise error
04:16:51 papermill.exceptions.PapermillExecutionError:
04:16:51 ---------------------------------------------------------------------------
04:16:51 Exception encountered at "In [6]":
04:16:51 ---------------------------------------------------------------------------
04:16:51 ValueError Traceback (most recent call last)
04:16:51 /tmp/ipykernel_20597/622294786.py in <module>
04:16:51 43 data=train_files, transform=train_transforms, cache_dir=persistent_cache
04:16:51 44 )
04:16:51 ---> 45 train_loader = monai.data.DataLoader(
04:16:51 46 train_ds, batch_size=2, shuffle=True, num_workers=2, pin_memory=True
04:16:51 47 )
04:16:51
04:16:51 /opt/conda/lib/python3.8/site-packages/monai/data/dataloader.py in __init__(self, dataset, num_workers, **kwargs)
04:16:51 82 kwargs.update({"worker_init_fn": worker_init_fn})
04:16:51 83
04:16:51 ---> 84 super().__init__(dataset=dataset, num_workers=num_workers, **kwargs)
04:16:51
04:16:51 /opt/conda/lib/python3.8/site-packages/torch/utils/data/dataloader.py in __init__(self, dataset, batch_size, shuffle, sampler, batch_sampler, num_workers, collate_fn, pin_memory, drop_last, timeout, worker_init_fn, multiprocessing_context, generator, prefetch_factor, persistent_workers)
04:16:51 266 else: # map-style
04:16:51 267 if shuffle:
04:16:51 --> 268 sampler = RandomSampler(dataset, generator=generator)
04:16:51 269 else:
04:16:51 270 sampler = SequentialSampler(dataset)
04:16:51
04:16:51 /opt/conda/lib/python3.8/site-packages/torch/utils/data/sampler.py in __init__(self, data_source, replacement, num_samples, generator)
04:16:51 100
04:16:51 101 if not isinstance(self.num_samples, int) or self.num_samples <= 0:
04:16:51 --> 102 raise ValueError("num_samples should be a positive integer "
04:16:51 103 "value, but got num_samples={}".format(self.num_samples))
04:16:51 104
04:16:51
04:16:51 ValueError: num_samples should be a positive integer value, but got num_samples=0
3d_registration/paired_lung_ct.ipynb
04:25:38 Running ./3d_registration/paired_lung_ct.ipynb
04:25:38 Checking PEP8 compliance...
04:25:39 Running notebook...
04:25:39 Before:
04:25:39 "max_epochs = 5\n",
04:25:39 After:
04:25:39 "max_epochs = 1\n",
04:25:39 Before:
04:25:39 "val_interval = 1\n",
04:25:39 After:
04:25:39 "val_interval = 1\n",
04:27:25
Executing: 0%| | 0/35 [00:00<?, ?cell/s]
Executing: 3%|▎ | 1/35 [00:01<00:51, 1.52s/cell]
Executing: 9%|▊ | 3/35 [00:05<01:01, 1.92s/cell]
Executing: 14%|█▍ | 5/35 [00:07<00:43, 1.45s/cell]
Executing: 26%|██▌ | 9/35 [00:46<02:44, 6.33s/cell]
Executing: 49%|████▊ | 17/35 [00:50<00:47, 2.64s/cell]
Executing: 54%|█████▍ | 19/35 [00:54<00:41, 2.58s/cell]
Executing: 60%|██████ | 21/35 [00:57<00:32, 2.35s/cell]
Executing: 71%|███████▏ | 25/35 [01:38<00:53, 5.32s/cell]
Executing: 80%|████████ | 28/35 [01:39<00:26, 3.83s/cell]
Executing: 89%|████████▊ | 31/35 [01:42<00:12, 3.08s/cell]
Executing: 89%|████████▊ | 31/35 [01:43<00:13, 3.35s/cell]
04:27:25 Traceback (most recent call last):
04:27:25 File "/opt/conda/bin/papermill", line 8, in <module>
04:27:25 sys.exit(papermill())
04:27:25 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
04:27:25 return self.main(*args, **kwargs)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1062, in main
04:27:25 rv = self.invoke(ctx)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
04:27:25 return ctx.invoke(self.callback, **ctx.params)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 763, in invoke
04:27:25 return __callback(*args, **kwargs)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
04:27:25 return f(get_current_context(), *args, **kwargs)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
04:27:25 execute_notebook(
04:27:25 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
04:27:25 raise_for_execution_errors(nb, output_path)
04:27:25 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
04:27:25 raise error
04:27:25 papermill.exceptions.PapermillExecutionError:
04:27:25 ---------------------------------------------------------------------------
04:27:25 Exception encountered at "In [15]":
04:27:25 ---------------------------------------------------------------------------
04:27:25 RuntimeError Traceback (most recent call last)
04:27:25 /tmp/ipykernel_25414/3442420488.py in <module>
04:27:25 1 resource = "https://drive.google.com/uc?id=1SUS8qknkxyF_lRLmjNqMz_DvH3Nygj68"
04:27:25 2 dst = f"{root_dir}/pretrained_weight.pth"
04:27:25 ----> 3 download_url(resource, dst)
04:27:25 4 model.load_state_dict(torch.load(dst))
04:27:25
04:27:25 /opt/conda/lib/python3.8/site-packages/monai/apps/utils.py in download_url(url, filepath, hash_val, hash_type, progress)
04:27:25 194 _download_with_progress(url, tmp_name, progress=progress)
04:27:25 195 if not tmp_name.exists():
04:27:25 --> 196 raise RuntimeError(
04:27:25 197 f"Download of file from {url} to {filepath} failed due to network issue or denied permission."
04:27:25 198 )
04:27:25
04:27:25 RuntimeError: Download of file from https://drive.google.com/uc?id=1SUS8qknkxyF_lRLmjNqMz_DvH3Nygj68 to /tmp/tmp8trh1cx2/pretrained_weight.pth failed due to network issue or denied permission.
./deepgrow/ignite/inference_3d.ipynb
02:46:26 Running ./deepgrow/ignite/inference_3d.ipynb
02:46:26 Checking PEP8 compliance...
02:46:27 Running notebook...
02:46:27 Before:
02:46:27 "max_epochs = 1\n",
02:46:27 After:
02:46:27 "max_epochs = 1\n",
02:46:44
Executing: 0%| | 0/7 [00:00<?, ?cell/s]
Executing: 14%|█▍ | 1/7 [00:05<00:30, 5.07s/cell]
Executing: 29%|██▊ | 2/7 [00:07<00:17, 3.51s/cell]
Executing: 43%|████▎ | 3/7 [00:12<00:15, 3.99s/cell]
Executing: 57%|█████▋ | 4/7 [00:15<00:11, 3.68s/cell]
Executing: 71%|███████▏ | 5/7 [00:15<00:04, 2.43s/cell]
Executing: 71%|███████▏ | 5/7 [00:16<00:06, 3.24s/cell]
02:46:44 Traceback (most recent call last):
02:46:44 File "/opt/conda/bin/papermill", line 8, in <module>
02:46:44 sys.exit(papermill())
02:46:44 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1137, in __call__
02:46:44 return self.main(*args, **kwargs)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1062, in main
02:46:44 rv = self.invoke(ctx)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
02:46:44 return ctx.invoke(self.callback, **ctx.params)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 763, in invoke
02:46:44 return __callback(*args, **kwargs)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
02:46:44 return f(get_current_context(), *args, **kwargs)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
02:46:44 execute_notebook(
02:46:44 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
02:46:44 raise_for_execution_errors(nb, output_path)
02:46:44 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
02:46:44 raise error
02:46:44 papermill.exceptions.PapermillExecutionError:
02:46:44 ---------------------------------------------------------------------------
02:46:44 Exception encountered at "In [5]":
02:46:44 ---------------------------------------------------------------------------
02:46:44 ValueError Traceback (most recent call last)
02:46:44 /tmp/ipykernel_7392/4109804221.py in <module>
02:46:44 1 # Evaluation
02:46:44 2 model_path = 'deepgrow_3d.ts'
02:46:44 ----> 3 model = jit.load(model_path)
02:46:44 4 model.cuda()
02:46:44 5 model.eval()
02:46:44
02:46:44 /opt/conda/lib/python3.8/site-packages/torch/jit/_serialization.py in load(f, map_location, _extra_files)
02:46:44 149 if isinstance(f, string_classes):
02:46:44 150 if not os.path.exists(f): # type: ignore[type-var]
02:46:44 --> 151 raise ValueError("The provided filename {} does not exist".format(f)) # type: ignore[str-bytes-safe]
02:46:44 152 if os.path.isdir(f):
02:46:44 153 raise ValueError("The provided filename {} is a directory".format(f)) # type: ignore[str-bytes-safe]
02:46:44
02:46:44 ValueError: The provided filename deepgrow_3d.ts does not exist
Metadata
Metadata
Assignees
Labels
No labels