Custom RT range + running averages

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9:46 AM

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May 22, 2012, 3:45:28 PM5/22/12
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Hello Stimfit community,


I've been really bugged by two questions, and I thought maybe somebody knew how to solve this :/

(a) Is it possible to make Stimfit calculate a custom RT (e.g., 10-50% instead of the default 20-80%)?

(b) How can one create running averages (e.g., not an average of the entire data set, but averages of every six traces)?


Thanks in advance!

Ilya Flyamer

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May 22, 2012, 3:52:52 PM5/22/12
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Hi!

I'm quite new to stimfit, but I think both cases need python scripting, thow (b) can be done via this:
http://www.stimfit.org/doc/sphinx/howto/runningmean.html?highlight=running%20average
As I understand, this funcrion does, what you need, thow I don't know, whether it works for more than one trace... Try it. In any case, it should work for one trace at a time.

Ilya.

2012/5/22 9:46 AM <urruua...@gmail.com>

Jose Guzman

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May 23, 2012, 3:32:19 AM5/23/12
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On 22/05/12 21:52, Ilya Flyamer wrote:
Hi!
(b) How can one create running averages (e.g., not an average of the entire data set, but averages of every six traces)?


The general strategy  is to define a Python function that operates on a given trace, and enter a list of traces as argument to that function. You can find an example in  http://www.stimfit.org/doc/sphinx/howto/amplitudes.html that calculates amplitudes on selected traces  in Stimfit.

I will give you a very basic example


import stf
import numpy as np

def get_mean(start, end, trace):
    """
    computes the average of the trace between
    start and end
  
    Arguments:
    start    -- starting points (in xunits)
    end     -- end point (in xunits)
    trace   -- zero-based index of the trace to calculate the mean

    Returns:
    mean value of the trace between start and end

    Example:
    >>> get_mean(0, 100, 0) # returns means between 0 and 100 in sweep 0
    >>> [get_mean(0, 100, sweep) for sweep in range(0, 100, 6)] # returns a list
    of averages of 100 sweeps every 6 trace
     """
  
    # type checking
    if type(trace) !=int:
        print("Trace arguments only admits integers")
        return False

    # check that sweep is not out of range
    if trace>stf.get_size_channel():
        print("Trace out of range")
        return False

    # transform time into sampling points
    dt = stf.get_sampling_interval()
    pstart = int(round(start/dt))
    pend = int(round(end/dt))

    # obtain average
    sweep = stf.get_trace(trace, channel=-1)[pstart:pend]
    avg = np.mean(sweep)
    return(avg)


As you can see in the example, you can enter a list of traces as argument with a list comprehension, or
alternatively with a for loop:
 
>>> mylist = range(0,100,6)
>>> for sweep in mylist:
>>>    get_mean(0, 100, sweep)

Hope it helps!

Jose
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