pyvista issue with point_arrays

[gusqgm]

Following up on the installation of the newest version of pyvista (currently 0.38.5), the following error occurs when running the ViewerTask as exemplified in the example part of the repository:

$ LUIGI_CONFIG_PATH=./config.cfg luigi --local-scheduler --module lstree ViewerTask
/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/improc/io.py:92: UserWarning: registration of accessor <class 'improc.io.DCAccessor'> under name 'dc' for type <class 'pandas.core.series.Series'> is overriding a preexisting attribute with the same name.
pd.api.extensions.register_series_accessor('dc')(cls)
/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/improc/io.py:93: UserWarning: registration of accessor <class 'improc.io.DCAccessor'> under name 'dc' for type <class 'pandas.core.frame.DataFrame'> is overriding a preexisting attribute with the same name.
pd.api.extensions.register_dataframe_accessor('dc')(cls)
INFO: Informed scheduler that task ViewerTask_cell_segmentatio___example_data___nuclei_segmentat_e2bdc17f32 has status PENDING
INFO: Done scheduling tasks
INFO: Running Worker with 16 processes
INFO: [pid 34738] Worker Worker(salt=444163483, workers=16, host=libws01.fmi.ch, username=quingust, pid=34695) running ViewerTask(movie_dirs=["example/data/-"], nuclei_seg_subdir=nuclei_segmentation, cell_seg_subdir=cell_segmentation)
INFO: [pid 34738] Worker Worker(salt=444163483, workers=16, host=libws01.fmi.ch, username=quingust, pid=34695) new requirements ViewerTask(movie_dirs=["example/data/-"], nuclei_seg_subdir=nuclei_segmentation, cell_seg_subdir=cell_segmentation)
INFO: Informed scheduler that task VolumeGridTask_max___gray____red___5_7677de0500 has status PENDING
INFO: Informed scheduler that task DeconvolutionTask_Channel0__9999__9999__999_experiment_json_1a1df7d1ad has status DONE
INFO: Informed scheduler that task DeconvolutionTask_Channel1__9999__9999__999_experiment_json_7638cd360d has status DONE
INFO: Informed scheduler that task ExternalInputFile_example_data_003_f395362fce has status DONE
INFO: Informed scheduler that task ViewerTask_cell_segmentatio___example_data___nuclei_segmentat_e2bdc17f32 has status PENDING
INFO: [pid 34742] Worker Worker(salt=444163483, workers=16, host=libws01.fmi.ch, username=quingust, pid=34695) running VolumeGridTask(movie_config_name=experiment.json, movie_dir=example/data/003-Enterocyst, raw_channel_subdirs=["Channel1", "Channel0"], colormaps=["gray", "red"], blending_mode=max, ref_mesh_subdir=cell_mesh, pattern={subdir}/{fname}-T{time:04d}.{ext}, out_subdir=rgb_grid, crop_margin=5, n_threads=3)
INFO: exporting img grid: example/data/003-Enterocyst/rgb_grid/grid-T0321.vti
INFO: exporting img grid: example/data/003-Enterocyst/rgb_grid/grid-T0322.vti
INFO: exporting img grid: example/data/003-Enterocyst/rgb_grid/grid-T0323.vti
INFO: exporting img grid: example/data/003-Enterocyst/rgb_grid/grid-T0324.vti
ERROR: [pid 34742] Worker Worker(salt=444163483, workers=16, host=libws01.fmi.ch, username=quingust, pid=34695) failed VolumeGridTask(movie_config_name=experiment.json, movie_dir=example/data/003-Enterocyst, raw_channel_subdirs=["Channel1", "Channel0"], colormaps=["gray", "red"], blending_mode=max, ref_mesh_subdir=cell_mesh, pattern={subdir}/{fname}-T{time:04d}.{ext}, out_subdir=rgb_grid, crop_margin=5, n_threads=3)
Traceback (most recent call last):
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/luigi/worker.py", line 191, in run
new_deps = self._run_get_new_deps()
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/luigi/worker.py", line 133, in _run_get_new_deps
task_gen = self.task.run()
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/lstree/segmentation/mesh_tasks.py", line 260, in run
monitor_futures(futures)
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/lstree/luigi_utils.py", line 55, in monitor_futures
return [f.result() for f in futures]
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/lstree/luigi_utils.py", line 55, in
return [f.result() for f in futures]
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/lstree/segmentation/mesh_tasks.py", line 228, in _img_to_grid
grid = rgb_stack_to_grid(rgb_img, self.spacing, bounds)
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/lstree/segmentation/mesh_tasks.py", line 47, in rgb_stack_to_grid
grid.point_arrays["values"] = rgb.reshape(-1, 3, order="F")
File "/tungstenfs/scratch/gliberal/Users/quingust/miniconda3/envs/ls3_jd/lib/python3.7/site-packages/pyvista/core/dataset.py", line 122, in getattr
return super().getattribute(item)
AttributeError: 'UniformGrid' object has no attribute 'point_arrays'
INFO: Informed scheduler that task VolumeGridTask_max___gray____red___5_7677de0500 has status FAILED
INFO: Worker Worker(salt=444163483, workers=16, host=libws01.fmi.ch, username=quingust, pid=34695) was stopped. Shutting down Keep-Alive thread
INFO:
===== Luigi Execution Summary =====

Scheduled 6 tasks of which:

• 3 complete ones were encountered:
  • 2 DeconvolutionTask(...)
  • 1 ExternalInputFile(path=example/data/003-Enterocyst/experiment.json)
• 1 failed:
  • 1 VolumeGridTask(...)
• 2 were left pending, among these:
  • 1 were missing external dependencies:
    • 1 ViewerTask(movie_dirs=["example/data/-"], nuclei_seg_subdir=nuclei_segmentation, cell_seg_subdir=cell_segmentation)
  • 1 was not granted run permission by the scheduler:
    • 1 ViewerTask(movie_dirs=["example/data/-"], nuclei_seg_subdir=nuclei_segmentation, cell_seg_subdir=cell_segmentation)

This progress looks :( because there were failed tasks

===== Luigi Execution Summary =====

this occurs because pyvista has migrated point_arrays -> point_data as explained in their issue #1779. Changing from to point_data in the mesh_tasks.py solves this issue.