Appion

I think we might be seeing a bug related to this. With some negative stain images, the database insertion is failing. Below is the error:

 ... Computing median of power spectra series
 ... Compute PSD with fieldsize 2048 and 9 images complete in 55.18 sec
!!! WARNING: Requested resolution (3.000) is not available (8.100)
 ... Preform a rotational average and remove spikes...
PART 1: SETUP PARAMETERS AND ELLIPTICAL AVERAGE
 ... Number of available peaks is 250
/panfs/storage.local/imb/stagg/software/myami_dev/appion/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 3.75 msec
Traceback (most recent call last):
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/pyace2.py", line 361, in <module>
    imgLoop.run()
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/appionLoop2.py", line 93, in run
    self.loopCommitToDatabase(imgdata)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/appionLoop2.py", line 143, in loopCommitToDatabase
    return self.commitToDatabase(imgdata)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/bin/pyace2.py", line 286, in commitToDatabase
    ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrundata, self.params['rundir'])
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
    ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfinsert.py", line 83, in runCTFdisplayTools
    ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfdisplay.py", line 1257, in makeCtfImages
    ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfdisplay.py", line 1139, in CTFpowerspec
    normpowerspec = self.normalizeCtf(powerspec, twod=twod)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfdisplay.py", line 210, in normalizeCtf
    fitvalleydata[startIndex:endIndex], "below")
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfnoise.py", line 550, in modelCTFNoise
    filterctfdata, contraintFunction)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfnoise.py", line 399, in getAllInitialParameters
    fitparams, value = self.fitLinear(xdata, ctfdata, contraintFunction)
  File "/panfs/storage.local/imb/stagg/software/myami_dev/appion/appionlib/apCtf/ctfnoise.py", line 183, in fitLinear
    z = numpy.polyfit(xdata, ctfdata, 1)
  File "/usr/lib64/python2.6/site-packages/numpy/lib/polynomial.py", line 551, in polyfit
    raise TypeError("expected non-empty vector for x")
TypeError: expected non-empty vector for x

The pixel size for these images is 4.05 and we can see one Thon ring. We aren't having any problems with cryo data.

Neil,

It occurs to me that the way you generate 1D plot can be applied to any image given. How about feed in the empty image from the algorithm Bob Glaeser suggested awhile ago, see Issue #2078. You should get a perfect 1D background to subtract. No fitting needed except the water ring itself which I would think will be easier once all other components are gone.

Hi Anchi, The background noise is not as difficult a problem as the envelope. But it would be interesting to try this.

The main issue is where I decide to cut the sections for the fit. In close to focus images there are not as many peaks and valleys that make good cut points.