"global" auto-CoR fails when scipy is not installed
For some reason the latest "global" auto-CoR fails when scipy is not installed.
Without scipy:
(2020.4.0) (base) lbs191:/nobackup/lbs191tmp1/nabu % nabu nabu.conf --slice middle
Matplotlib not available. Plotting disabled
Loaded flats/darks from /lbsram/pierre/nabu_processes.h5
Traceback (most recent call last):
File "/nobackup/lbs191tmp1/nabu/2020.4.0/bin/nabu", line 8, in <module>
sys.exit(main())
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/resources/cli/reconstruct.py", line 111, in main
proc = ProcessConfig(args["input_file"])
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/resources/processconfig.py", line 74, in __init__
self._get_cor()
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/resources/processconfig.py", line 87, in _get_cor
cor = self.corfinder.find_cor(search_method=cor)
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/resources/cor.py", line 120, in find_cor
shift = self.cor.find_shift(
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/preproc/alignment.py", line 787, in find_shift
cor_position = super(self.__class__, self).find_shift(
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/preproc/alignment.py", line 602, in find_shift
fitted_shifts_vh = self.refine_max_position_2d(f_vals, fv, fh)
File "/nobackup/lbs191tmp1/nabu/2020.4.0/lib/python3.8/site-packages/nabu/preproc/alignment.py", line 176, in refine_max_position_2d
raise ValueError(
ValueError: Fitted (y: -669.1166490950043, x: -98.29805309776903) positions are outide the input margins y: [-626.0, -624.0], and x: [-99.0, -97.0]
When scipy is installed, the auto-CoR goes smoothly:
(2020.4.0) (base) lbs191:/nobackup/lbs191tmp1/nabu % nabu nabu.conf --slice middle
Matplotlib not available. Plotting disabled
Loaded flats/darks from /lbsram/pierre/nabu_processes.h5
Overwriting config file start_z to 1080 and end_z to 1080
Going to reconstruct slices (1080, 1080)
Processing sub-volume (1080, 1081)
Estimated center of rotation: 454.50
File already exists: /lbsram/pierre/wobble_test_1_0001_rec/wobble_test_1_0001_rec_1080.hdf5. It will be overwritten as requested in configuration
Reading data
Applying flat-field
Taking logarithm
Building sinograms
Reconstruction
Saving data
Wrote /lbsram/pierre/wobble_test_1_0001_rec/wobble_test_1_0001_rec_1080.hdf5
File /lbsram/pierre/wobble_test_1_0001_rec.hdf5 already exists. Overwriting as requested in configuration file
Merging reconstructions to /lbsram/pierre/wobble_test_1_0001_rec.hdf5
There must be a difference in the implementation of some filter.
Edited by Pierre Paleo