scilus / freewater_flow Goto Github PK

Flow breaks on dti_metrics. Here is the error. Ran using scilpy master (not singularity)...

more work/9c/43822bf5e25a0c8d5bf43a469f3f62/.command.err
WARNING:root:Your b-vectors do not seem normalized...
/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/dipy/reconst/dti.py:498: RuntimeWarning: invalid value encountered in true_divide
return 3 * np.sqrt(6) * determinant((A_squiggle / A_s_norm))
INFO:Compute_DTI_Metrics:Not enough b=0 images to output standard deviation map
/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/dipy/reconst/dti.py:1955: RuntimeWarning: divide by zero encountered in log
D[..., 6] = -np.log(b0)
Traceback (most recent call last):
File "/home/descotea/my_env/scilpy_public/bin/scil_compute_dti_metrics.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/descotea/scilpy/scripts/scil_compute_dti_metrics.py", line 457, in
main()
File "/home/descotea/scilpy/scripts/scil_compute_dti_metrics.py", line 432, in main
figsize=[10, 4.8])
File "/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1184, in subplots
fig = figure(**fig_kw)
File "/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/matplotlib/pyplot.py", line 533, in figure
**kwargs)
File "/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 161, in new_figure_manager
return cls.new_figure_manager_given_figure(num, fig)
File "/home/descotea/my_env/scilpy_public/lib/python3.7/site-packages/matplotlib/backends/_backend_tk.py", line 1046, in new_figure_manager_given_figure
window = Tk.Tk(className="matplotlib")
File "/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/3.7.4/lib/python3.7/tkinter/init.py", line 2023, in init
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable

We must to add automount parameter in the config file.

default=1 sends to CPU as many freewater or noddi computations and explodes RAM. Does not seem like the best thing to do by default or otherwise, code should set maximum RAM allocated... or something