Re: [Pytom-mail] Extracting particles

[Dustin M. <dus...@gm...>]

Hi Kanika,

Are you also not getting any output? The output your talking about is just a warning.

sigma is generated by sqrt in the cmath module and so it can return a complex number, but “a” is calculated using exp from the math module which doesn’t work on complex numbers to it just discards the imaginary part and that’s what you’re seeing here.

FWIW from our experience with lots of different samples and data collected a lot of different ways, we never found a consistent way to estimate the number using a gaussian fit, and so we just extract more than we expect by a factor of about 5 and then remove false positives by classification.

HTH

—
Cheers,
Dustin

> On May 10, 2016, at 4:57 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Hi,
> 
> Can someone help me with the questions above. I am still trying to figure things out
> 
> Thanks! I appreciate your help.
> 
> On Sat, Apr 23, 2016 at 4:37 AM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
> The reason I ask this is I get this runtime error : /usr/local/pytom/tools/maths.py:652: ComplexWarning: Casting complex values to real discards the imaginary part
>   a=exp(a0+mu**2/(2*sigma**2)), whatever parameters I enter.
> 
> On Fri, Apr 22, 2016 at 4:03 PM, Kanika Khanna <kk...@uc... <mailto:kk...@uc...>> wrote:
> Hello all,
> 
> I am trying to estimate the no. of particles in tomogram by plotting the Gaussian plot. I extracted for instance, 1000 particles. What is the best way to optimize and determine the values of n (no. of bins), p (peak) and c (ccc value) in this case?
> 
> Thanks!
> 
> 
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