numpy.AxisError: axis2: axis 1 is out of bounds for array of dimension 1

[takrouni]

Hello Issam,
I have a problem when I execute the command: python3 extract_patches.py

Result:
Using TensorFlow backend.
iteration [0]
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/LGG/brats_tcia_pat282_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat222_0122
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat260_0129
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat394_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat265_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat153_0002
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat447_0199
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat231_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat374_0909
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat399_0217
iteration [10]
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat478_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_2013_pat0007_1
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat314_0290
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat117_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/LGG/brats_2013_pat0001_1
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_2013_pat0027_1
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat309_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat448_0001
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat444_0077
there is a problem here!!! the problem lies in this patient : Brats2017/Brats17TrainingData/HGG/brats_tcia_pat230_0481
Traceback (most recent call last):
File "extract_patches.py", line 249, in
Patches,Y_labels=pipe.sample_patches_randomly(num_patches,d, h, w)
File "extract_patches.py", line 87, in sample_patches_randomly
gt_im = np.swapaxes(self.train_im, 0, 1)[4]
File "/home/wiem/Bureau/tmp/CNNbasedMedicalSegmentation-master/.bashrc/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 585, in swapaxes
return _wrapfunc(a, 'swapaxes', axis1, axis2)
File "/home/wiem/Bureau/tmp/CNNbasedMedicalSegmentation-master/.bashrc/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
numpy.AxisError: axis2: axis 1 is out of bounds for array of dimension 1

Please help me

[gopalmani]

i have the same error . did you get this one?? need help

[gopalmani]

[karthikr87]

I am facing the same issue. Have you fixed it?

Using TensorFlow backend.
Traceback (most recent call last):
File "extract_patches.py", line 236, in
Patches,Y_labels=pipe.sample_patches_randomly(num_patches,d, h, w)
File "extract_patches.py", line 74, in sample_patches_randomly
gt_im = np.swapaxes(self.train_im, 0, 1)[4]
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 585, in swapaxes
return _wrapfunc(a, 'swapaxes', axis1, axis2)
File "/usr/local/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
numpy.AxisError: axis2: axis 1 is out of bounds for array of dimension 1

[rajdadia]

Make sure the system has enough RAM and storage and the file path is proper. The same error worked for me.

[sapnii2]

RAM and storage and the file path is proper but getting error same as takrouni

[ruchika61]

I faced the same problem . Please help