Running Plot 1 -- Plot 5: Successes and possible bugs

[awickert]

Notes on running examples in https://github.com/Loop3D/LoopStructural/tree/master/examples/1_basic, aside from #59.

• https://github.com/Loop3D/LoopStructural/blob/master/examples/1_basic/plot_1_data_prepration.py: Fully functional.
• https://github.com/Loop3D/LoopStructural/blob/master/examples/1_basic/plot_2_surface_modelling.py
  • Requires lavavu. I pip3 installed that.
  • I then upgraded my version of scikit-image from the Ubuntu system one to the newest one on pip3. Deprecation warnings removed. All good.
  • After this, I ran again, and received:

andy@cuesta:~/dataanalysis/LoopStructural/examples/1_basic$ python3 plot_2_surface_modelling.py 
2021-03-14 12:41:24,186 ~ LoopStructural.visualisation.model_visualisation ~ ERROR      ~ Plot area has not been defined.
2021-03-14 12:41:24,186 ~ LoopStructural.visualisation.model_visualisation ~ ERROR      ~ Plot area has not been defined.
2021-03-14 12:41:24,186 ~ LoopStructural.visualisation.model_visualisation ~ ERROR      ~ Plot area has not been defined.
Traceback (most recent call last):
  File "plot_2_surface_modelling.py", line 165, in <module>
    viewer.add_model_surfaces(cmap='tab20')
  File "/home/andy/.local/lib/python3.8/site-packages/LoopStructural/visualisation/model_visualisation.py", line 565, in add_model_surfaces
    cmap = cm.get_cmap(cmap,n_units)
UnboundLocalError: local variable 'cm' referenced before assignment

This seems like a potential bug.

• plot_3_model_visualisation.py: Success, and returned this image:
  
• plot_3_multiple_groups.py
  • Following error, installed pyamg with pip3. Add to dependencies?
  • Following this, the example remains nonfunctional:

andy@cuesta:~/dataanalysis/LoopStructural/examples/1_basic$ python3 plot_3_multiple_groups.py
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
2021-03-14 12:49:41,684 ~ LoopStructural.visualisation.model_visualisation ~ WARNING    ~ Isovalue doesn't exist inside bounding box
/home/andy/.local/lib/python3.8/site-packages/skimage/measure/_marching_cubes_lewiner.py:301: RuntimeWarning: invalid value encountered in greater
  if level < volume.min() or level > volume.max():
/home/andy/.local/lib/python3.8/site-packages/skimage/measure/_marching_cubes_lewiner.py:301: RuntimeWarning: invalid value encountered in less
  if level < volume.min() or level > volume.max():
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:135: RuntimeWarning: invalid value encountered in greater
  inside *= pos[:, i] > self.origin[None, i]
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:136: RuntimeWarning: invalid value encountered in less
  inside *= pos[:, i] < self.origin[None, i] + \
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:525: RuntimeWarning: invalid value encountered in floor_divide
  ix = ix // self.step_vector[None, 0]
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:526: RuntimeWarning: invalid value encountered in floor_divide
  iy = iy // self.step_vector[None, 1]
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:527: RuntimeWarning: invalid value encountered in floor_divide
  iz = iz // self.step_vector[None, 2]
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/interpolators/structured_tetra.py:197: RuntimeWarning: invalid value encountered in greater
  mask = np.all(c > 0, axis=2)
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/modelling/features/unconformity_feature.py:40: RuntimeWarning: invalid value encountered in less
  return self.feature.evaluate_value(pos) < self.value

• plot_4_using_stratigraphic_column.py

andy@cuesta:~/dataanalysis/LoopStructural/examples/1_basic$ python3 plot_4_using_stratigraphic_column.py
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/modelling/core/geological_model.py:1349: RuntimeWarning: invalid value encountered in less
  strat_id[np.logical_and(vals < series.get('max',feature.max()), vals > series.get('min',feature.min()))] = series['id']
/home/andy/.local/lib/python3.8/site-packages/LoopStructural/modelling/core/geological_model.py:1349: RuntimeWarning: invalid value encountered in greater
  strat_id[np.logical_and(vals < series.get('max',feature.max()), vals > series.get('min',feature.min()))] = series['id']

• plot_5_using_logging.py: Success, and returned two copies (default.png and default-00001.png -- perhaps a minor error here in the output code?) of this image: