voreille/hecktor

hecktor's Issues

wrong when using "evaluate_predictions.ipynb" to evaluate 3d dice

I found the evaluated result wrong when I used the code "evaluate_predictions.ipynb".After,I made a test. I used resampled gtvt data generated by the operation “python src/resampling/cli_resampling.py” as "prediction_folder" to evaluate 3d dice score,and I got the dice of 0.9528 instead of 1.Why?

using other DL framework

Could I use other DL framework to build model，such as Keras or Pytorch？

The validation dice is similar when 10% or 100% train datasets were used with the same validation sets.

Hello! I found an uncommon result.The validation results were similar when I used different numbers of patient case in 10% and 100% of training datasets.I have tested different codes, including this repository (the 3D dense_vnet result:23 train case:0.5914 ,180 train case:0.6233).At last, I got the same conclusion,especially in 2D,and the results are almost the same.
The case did not happen,when I used the type of dataset,which was randomly split as train and validation set in the way of shuffle all slices of all patient cases, instead of shuffling all patient cases.
Why ? The cause of data distribution？
I would appreciate you,if you can help me.Thanks!!!

baseline CNN (niftynet)

Hi,
I am interested in hecktor challenges although it is closed now. I am quite new to the idea of CNN. I see that it says there is a baseline CNN (niftynet) available in this repository but I cannot find it here. Is that deleted or could you share it with me? That would be very helpful. Thank you.

Resampling issue

I'm facing a problem in running python src/resampling/cli_resampling.py line.

C:\Users\x\y\hecktor_project\hecktor-master1>python src/resampling/cli_resampling.py
2020-07-02 22:30:28,050 - __main__ - INFO - Resampling
resampling is (1.0, 1.0, 1.0)
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexes\base.py", line 2646, in get_loc
    return self._engine.get_loc(key)
  File "pandas\_libs\index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas\_libs\hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'hecktor'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\multiprocessing\pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\multiprocessing\pool.py", line 48, in mapstar
    return list(map(*args))
  File "c:\users\x\y\hecktor_project\hecktor-master1\src\resampling\resampling.py", line 35, in __call__
    bb = (self.bb_df.loc[patient_name, 'x1'], self.bb_df.loc[patient_name,
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexing.py", line 1762, in __getitem__
    return self._getitem_tuple(key)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexing.py", line 1272, in _getitem_tuple
    return self._getitem_lowerdim(tup)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexing.py", line 1389, in _getitem_lowerdim
    section = self._getitem_axis(key, axis=i)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexing.py", line 1965, in _getitem_axis
    return self._get_label(key, axis=axis)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexing.py", line 625, in _get_label
    return self.obj._xs(label, axis=axis)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\generic.py", line 3537, in xs
    loc = self.index.get_loc(key)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\pandas\core\indexes\base.py", line 2648, in get_loc
    return self._engine.get_loc(self._maybe_cast_indexer(key))
  File "pandas\_libs\index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
  File "pandas\_libs\hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas\_libs\hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'hecktor'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "src/resampling/cli_resampling.py", line 76, in <module>
    main()
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "src/resampling/cli_resampling.py", line 68, in main
    p.map(resampler, files_list)
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\multiprocessing\pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "C:\Users\mahaw\AppData\Local\Programs\Python\Python38\lib\multiprocessing\pool.py", line 771, in get
    raise self._value
KeyError: 'hecktor'

Adding out-of-the-box cropping code of testing code.

There is no gtvt in testing sets.
Could you please updating the cropping code in the notebook?

Question about okapy.dicomconverter

Hi. I am getting "okapy.dicomconverter.converter" could not be resolved when I try to use make_dataset2022.py, (I have installed okapy using pip). Is the okapy library deprecated? Looking forward to your advice.

update crop_dataset.ipynb

Hi @voreille ,

Thanks for organizing the great challenge.
It seems that the cropping and resampling notebook has not been updated.
https://github.com/voreille/hecktor/blob/master/notebooks/crop_dataset.ipynb

Looking forward to your update:)

No module named 'src.resampling.utils'

When I try to run evaluate_predictions.ipynb in the notebook dir, I get the following message:

No module named 'src.resampling.utils'

I cannot find the module in the src directory. Is there any solution?

Error occurs when running baseline model

When I run "net_segment evaluation -c config3D.ini" after inference, "KeyError: ("label",)" was raised. I just followed the steps mentioned in README. Is there any solution to this problem?