Appion

I wonder if it is a out of memory error. Do all images fail or just some of them?

every image, on the CCD data too. Don't think it can be memory, we're running on the exact same systems as before, only change was the myami/trunk update.

Nothing has really changed in the apCtf folder (at least by me) since June 2016. Phase shifting does not work, or I have never tested it.

okay it's nothing with the code, it seems to have something to do with the python finagling we did to get the K2 webserver display stuff working. what a mess.

I'm having this problem too. We just updated our Python, numpy, scipy. Can y'all post what versions of those things y'all have? Here's my stuff.
[sstagg@krios-0-1 ctffind4run4]$ python
Python 2.7.5 (default, Nov 6 2016, 00:28:07)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

import scipy
scipy.__version__

'0.18.0'

import numpy
numpy.__version__

'1.12.0'

Scott, I think it may be a problem with matplotlib, but I don't know. These are my test environments:

CentOS 6 has:

scipy-0.7.2-8.el6.x86_64.rpm
numpy-1.4.1-9.el6.x86_64.rpm
python-matplotlib-0.99.1.2-1.el6.x86_64.rpm

CentOS 7 has:

numpy-1.7.1-11.el7.x86_64.rpm
scipy-0.12.1-3.el7.x86_64.rpm
python-matplotlib-1.2.0-15.el7.x86_64.rpm

Debian 8.8 has:

>>> numpy.__version__
'1.8.2'
>>> scipy.__version__
'0.14.0'
>>> matplotlib.__version__
'1.4.2'

Wow, your versions are quite new. I was going to test Debian 9 when it comes out next week, but I do not want to install from sources it gets messy too quick. Maybe there is a problem with the latest versions of the code, perhaps related to python3 compatibility.

Ugh. Our HPC just updated to CentOS 7. I have matplotlib 1.2.0. If I posted an 8K image here, could you test it on one of your systems? I can downgrade in a virtualenv if we can figure out a set of libraries that work.

Hi Scott, yes I can test it on my CentOS 7 system. I have my docker setup that is pretty portable too.

Oh, yeah. 300 keV, 2.7 mm, 1.29 apix.

Trunk. I didn't update the field size, though. How did you do that?

We talked about this earlier, I thought:

appion/appionlib/apCtf/ctfpower.py, line 35:

old version:

twopowerint = int(math.floor(twopowerfloat))
fieldsize = 2**twopowerint

new version:

twopowerint = int(math.floor(twopowerfloat))-1
fieldsize = 2**twopowerint

alternative version:

twopowerint = 0 #override in next step
fieldsize = 2048

Sorry, you told me about it, but I hadn't gotten around to trying it. I'll try it now, and see if that fixes it.

Still didn't work. Any other suggestions? I just updated trunk, and I'm using python 2.7.5 and

scipy.__version__

'0.18.0'

numpy.__version__

'1.12.0'

matplotlib.__version__

'1.2.0'

... ctf estimation completed in 20.11 sec
 ... reading 17may11c_07gr_04sq_044hl_02ex-pow.txt
 ... reading MRC: 17may11c_07gr_04sq_044hl_02ex-pow.mrc size:(1024, 1024) dtype:float32
 ... writing JPEG: 17may11c_07gr_04sq_044hl_02ex-pow.jpg
 ==== Committing data to database ==== 
 ... Committing ctf parameters for 17may11c_07gr_04sq_044hl_02ex to database
 ... Reading image...
[CTF param] def1: 2.904 um | def2: 2.911 um | angle: -67.7 | ampcontr 0.07 | defratio 1.003
[CTF param]   additional phase shift: 0.0 degrees 
Final params: def1: 2.904 um | def2: 2.911 um | angle: -67.7 | defratio 1.00
 ... Defocus Astig Percent Diff 0.13 -- 2.904, 2.911 um
Computing power spectra in 2048x2048 blocks................................................
 ... Compute PSD with 48 subfields and fieldsize 2048 complete in 60.92 sec
!!! WARNING: Logging images failing CtfdisplayTool to /lustre/cryo/lustre/appiondata/17may11c/ctf/ctffind4run5/failed_ctfdisplay_images.txt
[CTF run]   method: unknown | runname ctffind4run5
[CTF param] def1: 2.904 um | def2: 2.911 um | angle: -67.7 | ampcontr 0.07 | defratio 1.003
[CTF param]   additional phase shift: 0.0 degrees 

Anchi put it a grab all try/except, so we have to remove it to find the error.

appion/appionlib/apCtf/ctfinsert.py, line 109:

old

    try:
        ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
    except:
        appendFailedImage(rundir, imgdata, ctfvalues,'makeCtfImages exception')
        return ctfvalues

move it out of the try and test

    ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
    try:
        pass
    except:
        appendFailedImage(rundir, imgdata, ctfvalues,'makeCtfImages exception')
        return ctfvalues

Traceback (most recent call last):
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/bin/ctffind4.py", line 451, in <module>
    imgLoop.run()
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/appionLoop2.py", line 95, in run
    self.loopCommitToDatabase(imgdata)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/appionLoop2.py", line 153, in loopCommitToDatabase
    return self.commitToDatabase(imgdata)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/bin/ctffind4.py", line 380, in commitToDatabase
    ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/ctfinsert.py", line 48, in validateAndInsertCTFData
    ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/ctfinsert.py", line 109, in runCTFdisplayTools
    ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/ctfdisplay.py", line 1616, in makeCtfImages
    ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/ctfdisplay.py", line 1480, in CTFpowerspec
    powerspec, self.trimfreq = self.powerSpectra(image, ctfdata)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/ctfdisplay.py", line 1385, in powerSpectra
    genctfspec = genctf.generateCTF2dFromCtfData(ctfdata, adjusted_apix, self.volts, fieldsize)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/genctf.py", line 150, in generateCTF2dFromCtfData
    return generateCTF2d(focus1, focus2, theta, shape, mpix, cs, volts, ampconst, extra_phase_shift)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/genctf.py", line 179, in generateCTF2d
    radiisq = generateRadial2d(shape, xfreq, yfreq)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/genctf.py", line 322, in generateRadial2d
    r = Radial(halfshape, xfreq, yfreq, center=False)
  File "/panfs/storage.local/imb/stagg/software/myamiss/appion/appionlib/apCtf/genctf.py", line 302, in __init__
    self.radial = numpy.fromfunction(self.distance, shape, dtype=numpy.float64)
  File "/usr/lib64/python2.7/site-packages/numpy/core/numeric.py", line 2156, in fromfunction
    args = indices(shape, dtype=dtype)
  File "/usr/lib64/python2.7/site-packages/numpy/core/numeric.py", line 2094, in indices
    res = empty((N,)+dimensions, dtype=dtype)
TypeError: 'numpy.float64' object cannot be interpreted as an index

It is an issue with numpy v1.12 or later. Looking into a fix.

Fixed. Stupid error when the shape dimensions are not integers, see commit commit:8ef4b475

# fix for numpy 1.12 or newer
shape = numpy.array(shape, dtype=numpy.uint16)
self.angular = numpy.fromfunction(self.arctan, shape, dtype=numpy.float64)

That fixed it on my end.