Project-MONAI / Project-MONAI/tutorials
using collection names with spaces in them breaks tcia_dataset.ipynb
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Description
Describe the bug
In the "Create TciaDataset" step of the notebook if you enter a collection with spaces (e.g. "Lung Phantom") into the collection variable it produces an error. Here is the relevant part of the code:
Let's take the "QIN-PROSTATE-Repeatability" collection for example
collection, seg_type = "QIN-PROSTATE-Repeatability", "SEG"
Here is the error:
KeyError Traceback (most recent call last)
in
5 transform = Compose(
6 [
----> 7 LoadImaged(reader="PydicomReader", keys=["image", "seg"], label_dict=TCIA_LABEL_DICT[collection]),
8 ]
9 )
KeyError: 'Lung Phantom'
Environment (please complete the following information):
I was working on Google Colab
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Research direction
Start in tcia_dataset.ipynb at the “Create TciaDataset” step, examining TCIA_LABEL_DICT[collection] and the LoadImaged configuration. Reproduce the failure with the “Lung Phantom” collection in Google Colab; done means the notebook accepts collection names containing spaces without raising KeyError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100