Error when using reference-based boxing in EMAN 2.99.47
Mark Frank
Hello EMAN2 users,
I am Mark Frank, a Ph.D. candidate at Penn State. I am currently trying to average particles within a three-dimensional crystal contained within a cellular vesicle using the single particle tomography workflow in an effort to figure out what the identity of the constituent particles may be. I have obtained some interesting results when manually picking particles, but I would like to try my hand at a more automated method to see if the sample is as homogenous as it appears to be from several initial models where I changed the number of classes. To this end, I generated a new initial model by picking 30 representative particles in a new set and then used the output class from the new initial model generation pipeline into the reference-based workflow.
The output from e2version.py is as follows:
EMAN 2.99.47 ( GITHUB: 2023-03-04 21:22 - commit: NOT-INSTALLED-FROM-GIT-REPO )
Your EMAN2 is running on: Mac OS 14.4.1 x86_64
Your Python version is: 3.9.18
Hardware: 2021 MacBook Pro with M1 Pro SoC (10 CPU configuration), 16 GB Memory.
Command for making the initial model:
/users/markfrank/Applications/envs/eman2/bin/e2spt_sgd_new.py sets/initialpickforauto.lst --res=50.0 --niter=100 --shrink=1 --parallel=thread:10 --ncls=1 --batch=12 --learnrate=0.2 --sym=c1 --ppid=-2
The command used was for match picking:
/users/markfrank/Applications/envs/eman2/bin/e2spt_tempmatch.py tomograms/Position_1_2__bin4.hdf --reference=sptsgd_06/output_cls0.hdf --nptcl=500 --dthr=-1.0 --vthr=10.0 --minvol=-1 --maxvol=-1 --delta=30.0 --sym=c1 --rmedge --rmgold --boxsz=56 --threads=12 --ppid=-2
The error message from Terminal:
qt.apa.fonts: Populating font family aliases took 77 ms. Replace uses of missing font family "AppleSystemUIFont" with one that exists to avoid this cost.
NOT Writing notes, ppid=-2
Testing 588 orientations...
Locating reference-like particles in tomograms/Position_1_2__bin4.hdf (File 1/1)
Will shrink tomogram by 2
Will shrink reference by 8.0
588/588 finished.
removing edge: rotation 90.7
/users/markfrank/Applications/envs/eman2/bin/e2spt_tempmatch.py:170: DeprecationWarning: Please use 'sum' from the scipy. ndimage namespa ce, the 'scipy ndimage measurements' namespace is deprecated.
pks_vol = np.array(ndimage.measurements.sum/pks_mask, lb, list(range(1, nlb))))
0
Traceback (most recent call last) :
File "/users/markfrank/Applications/envs/eman2/bin/e2spt_tempmatch.py", line 279, in ‹module> main ( )
File "/users/markfrank/Applications/envs/eman2/bin/e2spt_tempmatch.py", line 195, in main pkscore/=np.max (pkscore)
File "<__array_function__
internals>", line 5, in amax
File "/users/markfrank/Applications/envs/eman2/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 2733, in amax return _wrapreduction(a, np.maximum, 'max', axis, None, out,
File "/users/markfrank/Applications/envs/eman2/1ib/python3.9/site-packages/numpy/core/fromnumeric.py", line 87, in wrapreduction return ufunc. reduce (obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity
Thank you in advance,
Mark A. Frank
Department of Biochemistry and Molecular Biology
Pennsylvania State University
Muyuan Chen
--
--
----------------------------------------------------------------------------------------------
You received this message because you are subscribed to the Google
Groups "EMAN2" group.
To post to this group, send email to em...@googlegroups.com
To unsubscribe from this group, send email to eman2+un...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/eman2
---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/4a73c6f2-66ed-4ef9-9b68-29f7a9fb0378n%40googlegroups.com.