LogNorm and vmin cannot be used simultaneously

[RemDelaporteMathurin]

plot = plot_regular_mesh_tally_with_geometry(
    tally=my_tally_xz,
    dagmc_file_or_trimesh_object="dagmc_not_merged.h5m",
    plane_origin=(0, 0, 0),
    plane_normal=[0, 1, 0],
    rotate_geometry=90,
    source_strength=source_strength,
    scale=LogNorm(),
    vmin=1e-3,
    label="Tritium generation (T/m3/s)",
    filename="my_tally_xz.png",
)

produces

  File "convert_results.py", line 24, in <module>
    plot = plot_regular_mesh_tally_with_geometry(
  File "/home/regular_mesh_plotter/regular_mesh_plotter/core.py", line 142, in plot_regular_mesh_tally_with_geometry
    plot = plot_regular_mesh_values(
  File "/home/regular_mesh_plotter/regular_mesh_plotter/core.py", line 48, in plot_regular_mesh_values
    image_map = plt.imshow(values, norm=scale, vmin=vmin, extent=extent, origin='lower')
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/_api/deprecation.py", line 456, in wrapper
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/pyplot.py", line 2640, in imshow
    __ret = gca().imshow(
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/_api/deprecation.py", line 456, in wrapper
    return func(*args, **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/__init__.py", line 1412, in inner
    return func(ax, *map(sanitize_sequence, args), **kwargs)
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/axes/_axes.py", line 5447, in imshow
    im._scale_norm(norm, vmin, vmax)
  File "/opt/conda/lib/python3.8/site-packages/matplotlib/cm.py", line 380, in _scale_norm
    raise ValueError(
ValueError: Passing parameters norm and vmin/vmax simultaneously is not supported. Please pass vmin/vmax directly to the norm when creating it.

[shimwell]

ah that is caused by this line, not quite sure how to apply vmin and scale separately.

https://github.com/fusion-energy/regular_mesh_plotter/blob/c5dbff275d56aaef8ec65fd7d85fc43091e6e8ee/regular_mesh_plotter/core.py#L48

[RemDelaporteMathurin]

So vmin and vmax only influence the colorbar.
If specifying the norm, you can do :

plot = plot_regular_mesh_tally_with_geometry(
    tally=my_tally_xz,
    dagmc_file_or_trimesh_object="dagmc_not_merged.h5m",
    plane_origin=(0, 0, 0),
    plane_normal=[0, 1, 0],
    rotate_geometry=90,
    source_strength=source_strength,
    scale=LogNorm(vmin=1e-3),
    label="Tritium generation (T/m3/s)",
    filename="my_tally_xz.png",
)

[RemDelaporteMathurin]

But vmin and vmax only change the colorbar, not the actual data, in the sense that it doesn't mask the data below or above this threshold.

It would be a very nice feature:
https://stackoverflow.com/questions/32991649/matplotlib-imshow-how-to-apply-a-mask-on-the-matrix

[RemDelaporteMathurin]

I think this will be fixed in #37