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Bug #3406

open

CTF display crashes on close to focus images

Added by Gabriel Lander about 9 years ago. Updated about 9 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Neil Voss
Category:
Image Processing
Target version:
-
Start date:
08/21/2015
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

We're running CTFFind on negative stain data that was collected very close to focus (~0.4 microns), and we get the attached error. We don't have this problem if we run myami/3.0

Beginning Main Loop

Starting image 1 ( skip:344, remain:67 ) id:3719578, file: 15aug17j_033sq_07hl_04en
... Pixel size: 2.05044
!!! WARNING: no best CTF value for image 15aug17j_033sq_07hl_04en
... Xmag=76081, dstep=1.56e-05, mpix=2.05e-10
!!! WARNING: Defocus minimum is less than zero
Defocus search range: 1000 A to 30000 A (0.10 to 3.00 um)
... running ctf estimation at Fri Aug 21 16:23:46 2015
/opt/applications/frealign/8.09/bin/ctffind64.exe
15aug17j_033sq_07hl_04en.mrc
15aug17j_033sq_07hl_04en-pow.mrc
2.2,120.0,0.15,76081.2313455,15.6,2
512,80.0,6.0,1000.0,30000.0,1000.0,500.0
... ctf estimation completed in 33.9 sec
... nominal=5.0e-07, bestdef=5.0e-07,
... def_1=6.1e-07, def_2=5.8e-07, astig_angle=-7.6, cross_corr=0.273,

... reading MRC: 15aug17j_033sq_07hl_04en-pow.mrc size:(512, 512) dtype:float32
 ... writing JPEG: 15aug17j_033sq_07hl_04en-pow.jpg
==== Committing data to database ==== 
 ... Committing ctf parameters for 15aug17j_033sq_07hl_04en to database
!!! WARNING: |def1| > |def2|, flipping defocus axes
 ... Reading image...
[CTF param] def1: 5.81e-07 | def2: 6.10e-07 | angle: 82.4 | ampcontr 0.15 | defratio 1.050
Final params: def1: 5.81e-07 | def2: 6.10e-07 | angle: 82.4 | defratio 1.05
 ... Defocus Astig Percent Diff 2.43 -- 5.809e-07, 6.099e-07
/opt/applications/python/lib/python2.6/site-packages/numpy-1.9.1-py2.6-linux-x86_64.egg/numpy/core/numeric.py:1846: DeprecationWarning: using a non-integer number instead of an integer wi
ll result in an error in the future
  res = empty((N,)+dimensions, dtype=dtype)
/opt/applications/python/lib/python2.6/site-packages/numpy-1.9.1-py2.6-linux-x86_64.egg/numpy/core/numeric.py:1849: DeprecationWarning: using a non-integer number instead of an integer wi
ll result in an error in the future
  tmp.shape = (1,)*i + (dim,)+(1,)*(N-i-1)
/opt/applications/python/lib/python2.6/site-packages/numpy-1.9.1-py2.6-linux-x86_64.egg/numpy/core/numeric.py:1851: DeprecationWarning: using a non-integer number instead of an integer wi
ll result in an error in the future
  val = zeros(newdim, dtype)
Computing power spectra in 2048x2048 blocks./opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfpower.py:101: DeprecationWarning: using a non-integer number inste
ad of an integer will result in an error in the future
  cutout = image[x1:x2, y1:y2]
........
 ... Computing median of power spectra series
 ... Compute PSD with fieldsize 2048 and 9 images complete in 22.18 sec
!!! WARNING: Requested resolution (3.000) is not available (4.101)
 ... Preform a rotational average and remove spikes...
PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE
 ... Number of available peaks is 24
/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctftools.py:490: DeprecationWarning: using a non-integer number instead of an integer will result in an error in 
the future
  xdataint = xdataint[:outercutsize]
 ... Determine and subtract noise model
PART 2: BACKGROUND NOISE SUBTRACTION
 ... starting peak extension
Peak Extension Complete in 0.88 msec

Found 0 ctf values
Traceback (most recent call last):
File "/opt/applications/myami/trunk/bin/ctfestimate.py", line 445, in <module>
imgLoop.run()
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 93, in run
self.loopCommitToDatabase(imgdata)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 143, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/opt/applications/myami/trunk/bin/ctfestimate.py", line 345, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 1257, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 1139, in CTFpowerspec
normpowerspec = self.normalizeCtf(powerspec, twod=twod)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfdisplay.py", line 210, in normalizeCtf
fitvalleydata[startIndex:endIndex], "below")
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfnoise.py", line 550, in modelCTFNoise
filterctfdata, contraintFunction)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfnoise.py", line 399, in getAllInitialParameters
fitparams, value = self.fitLinear(xdata, ctfdata, contraintFunction)
File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apCtf/ctfnoise.py", line 183, in fitLinear
z = numpy.polyfit(xdata, ctfdata, 1)
File "/opt/applications/python/lib/python2.6/site-packages/numpy-1.9.1-py2.6-linux-x86_64.egg/numpy/lib/polynomial.py", line 552, in polyfit
raise TypeError("expected non-empty vector for x")
TypeError: expected non-empty vector for x

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 #1

Updated by Neil Voss about 9 years ago

This error occurs because there were not enough points to fit, usually because it is very close to focus. I will take a look.

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 #2

Updated by Neil Voss about 9 years ago

  • Status changed from Assigned to In Test
  • Assignee changed from Neil Voss to Gabriel Lander

workaround in r19102

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 #3

Updated by Neil Voss about 9 years ago

  • Subject changed from incomprehensible error in ctffind to CTF display crashes on close to focus images
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 #4

Updated by Gabriel Lander about 9 years ago

  • Status changed from In Test to Assigned
  • Assignee changed from Gabriel Lander to Neil Voss

Got this error on a close-to focus image, not sure if it's related.

!!! WARNING: skipped 67 of 296 images
... [[ 0 no reprocess | 67 rejected | 0 wrong tilt | 0 in donedict ]]
... Process images old to new
... Running program ctffind64.exe

Beginning Main Loop

Starting image 1 ( skip:67, remain:228 ) id:3729587, file: stack_upload-a15aug27csy_screen_FoilHole_
28620941_Data_28613315_28613316_20150828_0807_frames
... Pixel size: 0.969079469448
[CTF run] method: ctffind | runname ctffindrun1
[CTF param] def1: 1.61e-06 | def2: 1.63e-06 | angle: 13.4 | ampcontr 0.07 | defratio 1.012
[CTF stats] conf_30-10: 0.931 | conf_5peak: 0.878 | res_0.8: 10.2A | res_0.5 6.
0A
... Xmag=150000, dstep=1.45e-05, mpix=9.69e-11
!!! WARNING: Defocus minimum is less than zero
Defocus search range: 1000 A to 41145 A (0.10 to 4.11 um)
... running ctf estimation at Mon Aug 31 12:07:06 2015
/gpfs/home/glander/myami/appion/bin/ctffind64.exe
stack_upload-a15aug27csy_screen_FoilHole_28620941_Data_28613315_28613316_20150828_0807_frames.mr
c
stack_upload-a15aug27csy_screen_FoilHole_28620941_Data_28613315_28613316_20150828_0807_frames-po
w.mrc
2.7,200.0,0.07,150000.0,14.5361920417,2
512,100.0,10.0,1000.0,41145.4,1000.0,500.0
... ctf estimation completed in 25.1 sec
... nominal=2.0e-06, bestdef=1.6e-06,
... def_1=1.6e-06, def_2=1.6e-06, astig_angle=-14.7, cross_corr=0.246,

... reading MRC: stack_upload-a15aug27csy_screen_FoilHole_28620941_Data_28613315_28613316_20150828_
0807_frames-pow.mrc size:(512, 512) dtype:float32
 ... writing JPEG: stack_upload-a15aug27csy_screen_FoilHole_28620941_Data_28613315_28613316_20150828
_0807_frames-pow.jpg
==== Committing data to database ==== 
 ... Committing ctf parameters for stack_upload-a15aug27csy_screen_FoilHole_28620941_Data_28613315_2
8613316_20150828_0807_frames to database
 ... Reading image...
[CTF param] def1: 1.61e-06 | def2: 1.64e-06 | angle: 14.7 | ampcontr 0.07 | defratio 1.018
Final params: def1: 1.61e-06 | def2: 1.64e-06 | angle: -14.7 | defratio 1.02
 ... Defocus Astig Percent Diff 0.90 - 1.612e-06, 1.642e-06
Computing power spectra in 2048x2048 blocks.........
 ... Computing median of power spectra series
 ... Compute PSD with fieldsize 2048 and 9 images complete in 13.45 sec
 ... Preform a rotational average and remove spikes...
PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE
 ... Number of available peaks is 195
 ... Determine and subtract noise model
PART 2: BACKGROUND NOISE SUBTRACTION
 ... starting peak extension
Peak Extension Complete in 1.48 msec
['/gpfs/home/glander/myami/appion/appionlib', '/gpfs/home/glander/myami/appion']
Found 1 ctf values
0.098 -- ctffindrun1
  • 0.098
    Traceback (most recent call last):
    File "/gpfs/home/glander/myami/appion/bin/ctfestimate.py", line 449, in <module>
    imgLoop.run()
    File "/gpfs/home/glander/myami/appion/appionlib/appionLoop2.py", line 93, in run
    self.loopCommitToDatabase(imgdata)
    File "/gpfs/home/glander/myami/appion/appionlib/appionLoop2.py", line 143, in loopCommitToDatabase
    return self.commitToDatabase(imgdata)
    File "/gpfs/home/glander/myami/appion/bin/ctfestimate.py", line 349, in commitToDatabase
    ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
    File "/gpfs/home/glander/myami/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsert
    CTFData
    ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
    File "/gpfs/home/glander/myami/appion/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTool
    s
    ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
    File "/gpfs/home/glander/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1267, in makeCtfImages
    ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
    File "/gpfs/home/glander/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1149, in CTFpowerspec
    normpowerspec = self.normalizeCtf(powerspec, twod=twod)
    File "/gpfs/home/glander/myami/appion/appionlib/apCtf/ctfdisplay.py", line 244, in normalizeCtf
    scale /= scale.max()
    ValueError: zero-size array to maximum.reduce without identity
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