rdrighetto
commented
7 years ago Dear EthanJUCB,
Thanks for your interest in FOCUS! The error you are getting is because you are using a version of NumPy that does not contain fft.rfftfreq. In my experience this often happens if your script is using the EMAN2 Python environment, but can also happen for other reasons. Have you configured FOCUS to find your EMAN2 installation? If so, you can test whether removing the path to EMAN2 fixes the problem (Settings >> Software >> EMAN2 installation directory). Also, you can explicitly check which NumPy the scripts are finding by inserting the following line in the script SPR_ExtractParticles.py right after the def main() line (double-click on the script filename under "Dependent Scripts" on the FOCUS GUI to open it in your text editor):
print np.path
The unbending CC profile is used to identify the particle positions in the micrograph, but they are extracted from the raw images. Please note that extracting particles from 2D crystals for processing with RELION and FREALIGN is still an experimental feature, and we are working on a publication of the method.
Please let me know if it works. I will anyway work on a robust version checking to avoid this error.
-- Ricardo Diogo Righetto
2017-05-19 0:33 GMT+02:00 EthanJUCB notifications@github.com:
Hi all,
I am trying to extract boxes from one micrograph. It worked perfectly when I extracted boxes for Relion in the absence of phase flipping. However, It didn't work when I checked the box "save as phase flipped stack" or "save as CTF-multiplied stack"or "save as Weiner filtered stack" and got errors as attached.
The other settings were"SPR_whichhalfset=crystalbased" "SPR_whichtiltgeometry=defocus" "SPR"whichCTF=Particle".
I also wonder if the boxes are extraced from unbent image or the raw image. Any suggestion will be appreciated. Many thanks
Traceback_** (most recent call last): File "/opt/focus/scripts/proc/SPR_ExtractParticles.py", line 1100, in main() File "/opt/focus/scripts/proc/SPR_ExtractParticles.py", line 480, in main boxctfcor = CTF.CorrectCTF( box, DF1=RLDEF1, DF2=RLDEF2, AST=params['AST_ANGLE'], WGH=ampcontrast, apix=apix, Cs=microscope_cs, kV=microscope_voltage, phase_flip=True, return_ctf=False, invert_contrast=False )[0] File "/opt/focus/scripts/proc/focus_ctf.py", line 102, in CorrectCTF CTFim = -CTF( img.shape, DF1, DF2, AST, WGH, Cs, kV, apix, 0.0, rfft ) File "/opt/focus/scripts/proc/focus_ctf.py", line 54, in CTF ymesh = np.fft.rfftfreq( imsize[1] ) AttributeError: 'module' object has no attribute 'rfftfreq' [1] Exit 1 /usr/bin/python /opt/focus/scripts/proc/SPR_ExtractParticles.py ../ SPR/2dx_merge_dirfile-unique.dat SPR/picking/ SPR/stacks/ particles 100 0.0,360 0.87 300.0 2.6 0.9975 58000 0 y y n y n n 0.4 1.0 0.90 Defocus Particle y y 1 1 Now organizing and converting partial stack(s) to single .mrcs and .par files... Done! Done!
Done!
########################ExportParticleStack finished.#####################
_**
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Hi all,
I am trying to extract boxes from one micrograph. It worked perfectly when I extracted boxes for Relion in the absence of phase flipping. However, It didn't work when I checked the box "save as phase flipped stack" or "save as CTF-multiplied stack"or "save as Weiner filtered stack" and got errors as attached.
The other settings were"SPR_whichhalfset=crystalbased" "SPR_whichtiltgeometry=defocus" "SPR"whichCTF=Particle".
I also wonder if the boxes are extraced from unbent image or the raw image. Any suggestion will be appreciated. Many thanks