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imr-framework / LFsim

Low-field MRI simulator
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ValueError: cannot reshape array of size 634880 into shape (256,256,120) #3

Open alvinkimbowa opened 1 year ago

alvinkimbowa commented 1 year ago

I utilized the keaDataProcessing.py provided with the Axial 10 days dataset in the Code folder to overcome one of the issues I raised before about that module not being found.

Then, I set up the paths in the LFsim/LF_sim_NHP_v5.py file as follows;

image_path_HF = r"/content/high_field_data/IXI016-Guys-0697-IXIT2WTS_-s231_-0401-00004-000002-02.nii"
LF_sim_saving_path = r"/content/lf_simulated_data"
image_path_LF = r"/content/drive/MyDrive/Axial_10days/Day1_01032023/Session1_11AM/3DTSE/1/data.3d"
acqu_path     = r"/content/drive/MyDrive/Axial_10days/Day1_01032023/Session1_11AM/3DTSE/1/acqu.par"
noise_path    = r"/content/drive/MyDrive/Axial_10days/Day1_01032023/Session1_11AM/3DTSE/1"

The high field image I'm using is from the IXI dataset (1 nifti file). The low field image I'm using is from the Axial_10 dataset. These can be deduced from the paths above. The axial 10 dataset is in volumes of 155x155x25 whereas the IXI dataset is in shapes of 256x256x120.

When I then run the LFsim/LF_sim_NHP_v5.py, it throws this error

Traceback (most recent call last):
  File "/content/LFsim/LF_sim_NHP_v5.py", line 307, in <module>
    LF_acq_noise_patch = get_noise(LF_sim, LF_noise_matrix, noise_fact)
  File "/content/LFsim/LF_simulation_functions.py", line 191, in get_noise
    LF_noise_use = np.reshape(LF_noise_use, (x,y,z))
  File "<__array_function__ internals>", line 180, in reshape
  File "/usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py", line 298, in reshape
    return _wrapfunc(a, 'reshape', newshape, order=order)
  File "/usr/local/lib/python3.10/dist-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
    return bound(*args, **kwds)
ValueError: cannot reshape array of size 634880 into shape (256,256,120)

I think this error arises from the difference in shapes between the IXI dataset and the Axial 10 dataset.

KunalTUM commented 1 year ago

This error came to me before as well. But then I realized that my numpy library still needed to be updated. When I did it, this error was gone. So you might have the same problem. Try updating your Numpy library.