Error while running "python train_2D.py"

[rhoadesScholar]

Discussed in #75

^{Originally posted by rajpiyush18 December 24, 2024}
I am getting the following error while running python train_2D.py

Sampling box shape is <= 0 for axis y with size -14. Setting to 1 and padding.
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0
Error: len() should return >= 0

Thereafter, the training proceeds normally. However, when Validation starts, I get the following error:

_Traceback (most recent call last):
File "C:\Users\plato\OneDrive - Mass General Brigham\Projects\CellMap_challenge\cellmap-segmentation-challenge\examples\train_2D.py", line 79, in
train(file)
File "C:\Users\plato\OneDrive - Mass General Brigham\Projects\CellMap_challenge\cellmap-segmentation-challenge\src\cellmap_segmentation_challenge\train.py", line 290, in train
for batch in val_bar:
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data\dataloader.py", line 701, in next
data = self._next_data()
^^^^^^^^^^^^^^^^^
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data\dataloader.py", line 757, in _next_data
data = self.dataset_fetcher.fetch(index) # may raise StopIteration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data_utils\fetch.py", line 50, in fetch
data = self.dataset.getitems(possibly_batched_index)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data\dataset.py", line 420, in getitems
return [self.dataset[self.indices[idx]] for idx in indices]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data\dataset.py", line 420, in
return [self.dataset[self.indices[idx]] for idx in indices]
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File "C:\Users\plato\miniforge3\envs\cellmap_hhmi\Lib\site-packages\torch\utils\data\dataset.py", line 350, in getitem
return self.datasets[dataset_idx][sample_idx]
~~~~~~~~~~~~~^^^^^^^^^^^^^
IndexError: list index out of range

My system configuration:
Windows 11 Laptop, 64 GB RAM, i9-12th Gen, Nvidia GeForce RTX 3070 Ti Laptop GPU
Running through miniforge prompt

[rhoadesScholar]

@rajpiyush18 can you post the contents of the datasplit.csv that was generated?

[rajpiyush18]

Attaching the datasplit.csv file
datasplit.csv

[rhoadesScholar]

My apologies. It seems that the bugs aren't all worked out on Windows yet. This is an issue with how file paths are parsed in the utilities. I should be able to clear it up Monday, if not before.