Final Project - 3D fMRI viewer

[G-S-Baz]

https://github.com/G-S-Baz/3D-fMRI-viewer

[szabgab]

The requirements.txt should only contain the names of the packages, no need for the "For the code to run, the following python packages should be installed:" it is actually bad to have it there as python will think that is also something to install.

Add pip install -r requirements.txt to the readme

Also I got this error: Please install the scikit-image package (instead of skimage)

$ python STR_viewer_main.py 
Traceback (most recent call last):
  File "/home/gabor/work/3D-fMRI-viewer/Code/STR_viewer_main.py", line 3, in <module>
    from striatum_viewer_ui import STRviewerUI
  File "/home/gabor/work/3D-fMRI-viewer/Code/striatum_viewer_ui.py", line 5, in <module>
    import striatum_viewer_supporting_functions as sf
  File "/home/gabor/work/3D-fMRI-viewer/Code/striatum_viewer_supporting_functions.py", line 33
    % loading the 4D fMRI data
                  ^
SyntaxError: invalid decimal literal

That % on some of the lines is incorrect.

Please fix these and comment here when you pushed out the fixed code.

[szabgab]

Also there is no .gitigrnore file.

[G-S-Baz]

Hi,
I fixed (hopefully) those issues.
Thanks,
Guy

[szabgab]

Now I get this:

Traceback (most recent call last):
  File "/home/gabor/work/3D-fMRI-viewer/Code/STR_viewer_main.py", line 3, in <module>
    from striatum_viewer_ui import STRviewerUI
  File "/home/gabor/work/3D-fMRI-viewer/Code/striatum_viewer_ui.py", line 5, in <module>
    import striatum_viewer_supporting_functions as sf
  File "/home/gabor/work/3D-fMRI-viewer/Code/striatum_viewer_supporting_functions.py", line 4, in <module>
    from stl import mesh
ImportError: cannot import name 'mesh' from 'stl' (/home/gabor/work/3D-fMRI-viewer/venv/lib/python3.11/site-packages/stl/__init__.py)

Are you sure we need str and not numpy-stl ?

[szabgab]

After installing numpy-stl I could run the program (Fix it in requirements.txt !)

I selected the 3 files via the GUI and got this on the command line. This does not look good.

Selected Files:
STR R: /home/gabor/work/3D-fMRI-viewer/ExampleData/rwSTR_R_prob_mni_non_linear_young.nii
STR L: /home/gabor/work/3D-fMRI-viewer/ExampleData/rwSTR_L_prob_mni_non_linear_young.nii
fMRI: /home/gabor/work/3D-fMRI-viewer/ExampleData/swTmaps_1-10.nii
X Error of failed request:  BadWindow (invalid Window parameter)
  Major opcode of failed request:  12 (X_ConfigureWindow)
  Resource id in failed request:  0x2
  Serial number of failed request:  7
  Current serial number in output stream:  8

[G-S-Baz]

Oh... that is bad.
I tried to look for it online...
Maybe it has something to do with linux?
see: pyvista/pyvistaqt#239.
There is a mention of "Wayland display server" in that link,
and also here: pyvista/pyvistaqt#445,
and here: https://gitlab.kitware.com/vtk/vtk/-/issues/18701.
I will try running the program on a mac computer I have to make sure it works,
Guy

[szabgab]

I recommend you add logging so we can see where does the crash happen. You can use either plain print statement or the logging module of Python. The latter is better.

There is no .gitignore file (there is one called .gitigrnore. That does not do much. I see it was my typo above. Sorry for that. Rename the file.