gausspyplus
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mriener
Crash in step 6
Though I could run the demo version of gausspy+-0.2dev0 under py3.8.7, scipy1.6.0, numpy1.19.5 and lmfit1.0.1, on a Mac OS10.12.6 (Sierra), when I applied it to my own dataset (13CO 1-0 spectra of a single cloud), it crashed in step 6. It is difficult to report the problem because the iterations are written upward on the screen, erasing all the initial information. I kill the job before the iterations start to get the initial information but the end is more problematic to collect.
OTF>python step_6_13co_10_spatial_refit2--grs.py
=========================== Spatial refitting - Phase 2
Flagging:
- Blended components: True
- Negative residual features: True
- Broad components: True
flagged if FWHM of broadest component in spectrum is:
= 2.0 times the FWHM of second broadest component or = 2.0 times any FWHM in >= 50% of its neigbors
- High reduced chi2 values (> None): False
- Non-Gaussian distributed residuals: True
- Differing number of components: True
threshold for required components: 0.833
Flags:
- 759 spectra w/ blended components
- 92 spectra w/ negative residual feature
- 1434 spectra w/ broad feature (info: 16 spectra w/ a FWHM > 57 channels)
- 0 spectra w/ high rchi2 value
- 1081 spectra w/ residual not passing normality test
- 121 spectra w/ differing number of components
check which spectra require refitting...
determine neighbors for all spectra... 12537it [00:10, 1165.48it/s]
start refit iteration #1... Using 6 of 8 cpus 6%|âââ | 721/12.5k [00:00<00:07, 1.51kit/s]
then it starts writing upwards... (not very convenient !): [...] 46%|ââââââââââââââââââ | 5.72k/12.5k [03:02<05:06, 22.2it/s] 43%|âââââââââââââââââ | 5.42k/12.5k [02:47<03:03, 38.8it/s] 43%|âââââââââââââââââ | 5.40k/12.5k [02:47<04:07, 28.9it/s] 41%|ââââââââââââââââ | 5.09k/12.5k [02:36<02:08, 57.7it/s] 41%|ââââââââââââââââ | 5.08k/12.5k [02:35<01:29, 82.9it/s] 41%|ââââââââââââââââ | 5.05k/12.5k [02:35<02:00, 62.0it/s] 38%|âââââââââââââââ | 4.77k/12.5k [02:27<01:44, 74.3it/s] 38%|âââââââââââââââ | 4.76k/12.5k [02:27<01:57, 66.3it/s] [...] and finally :
100%|ââââââââââââââââââââââââââââââââââââââ| 12.5k/12.5k [07:06<00:00, 29.4it/s] 12534it [00:00, 427489.74it/s] ââââââââââââ| 12.1k/12.5k [07:02<00:00, 1.08kit/s] SUCCESS ââââââââââââââââââââââââââââââââââ | 11.3k/12.5k [07:01<00:03, 331it/s]
it seems to have finished with these iterations. The output is mixed with the iteration report and in the end we get (I boldface the useful part, to separate from the iteration leftovers):
check which spectra require refitting... | 8.71k/12.5k [06:19<03:41, 17.3it/s]
Traceback (most recent call last): | 8.70k/12.5k [06:18<02:47, 22.9it/s]
File "step_6_13co_10_spatial_refit2--grs.py", line 86, in
so its index goes too far by a relatively large amount...
