# Physics307L F09:People/Trujillo/LAB NOTEBOOK/071003

### Raw Data Files

- File:Dwell20ms.asc
- File:Dwell40ms.asc
- File:Dwell80ms.asc
- File:Dwell100ms.asc
- File:Dwell200ms.asc
- File:Dwell400ms.asc
- File:Dwell800ms.asc
- File:Dwell1s.asc
- File:Dwell10s.asc

10ms

Oct 03 2007 03:07:41 am Elt: 000000 Seconds. Real Time: 000000 ID: No spectrum identifier defined Memory Size: 16384 Chls Conversion Gain: 1024 Adc Offset: 0000 Chls Chn Counts ROI 0, 0, 000 1, 0, 000 2, 0, 000 3, 0, 000 4, 0, 000 5, 0, 000 6, 0, 000 7, 0, 000 8, 0, 000 9, 0, 000 10, 0, 000 11, 0, 000 12, 0, 000 13, 0, 000 14, 0, 000 15, 0, 000 16, 0, 000 17, 0, 000 18, 0, 000 19, 0, 000 20, 0, 000 21, 0, 000 22, 0, 000 23, 0, 000 24, 0, 000 25, 0, 000 26, 0, 000 27, 0, 000 28, 0, 000 29, 0, 000 30, 0, 000 31, 0, 000 32, 0, 000 33, 0, 000 34, 0, 000 35, 0, 000 36, 0, 000 37, 0, 000 38, 0, 000 39, 0, 000 40, 0, 000 41, 0, 000 42, 0, 000 43, 0, 000 44, 0, 000 45, 0, 000 46, 0, 000 47, 0, 000 48, 0, 000 49, 0, 000 50, 0, 000 51, 0, 000 52, 0, 000 53, 0, 000 54, 0, 000 55, 0, 000 56, 0, 000 57, 0, 000 58, 0, 000 59, 0, 000 60, 0, 000 61, 0, 000 62, 0, 000 63, 0, 000 64, 1, 000 65, 0, 000 66, 0, 000 67, 0, 000 68, 0, 000 69, 0, 000 70, 0, 000 71, 0, 000 72, 0, 000 73, 0, 000 74, 0, 000 75, 0, 000 76, 0, 000 77, 0, 000 78, 0, 000 79, 0, 000 80, 0, 000 81, 0, 000 82, 0, 000 83, 0, 000 84, 0, 000 85, 0, 000 86, 0, 000 87, 0, 000 88, 0, 000 89, 0, 000 90, 0, 000 91, 0, 000 92, 0, 000 93, 0, 000 94, 0, 000 95, 0, 000 96, 0, 000 97, 0, 000 98, 0, 000 99, 0, 000 100, 0, 000 101, 0, 000 102, 0, 000 103, 0, 000 104, 0, 000 105, 0, 000 106, 1, 000 107, 0, 000 108, 0, 000 109, 0, 000 110, 0, 000 111, 0, 000 112, 0, 000 113, 0, 000 114, 0, 000 115, 0, 000 116, 0, 000 117, 0, 000 118, 0, 000 119, 0, 000 120, 0, 000 121, 0, 000 122, 0, 000 123, 0, 000 124, 0, 000 125, 0, 000 126, 0, 000 127, 0, 000 128, 0, 000 129, 0, 000 130, 0, 000 131, 0, 000 132, 0, 000 133, 0, 000 134, 0, 000 135, 0, 000 136, 0, 000 137, 0, 000 138, 0, 000 139, 0, 000 140, 0, 000 141, 0, 000 142, 0, 000 143, 0, 000 144, 0, 000 145, 0, 000 146, 1, 000 147, 0, 000 148, 0, 000 149, 0, 000 150, 0, 000 151, 0, 000 152, 0, 000 153, 0, 000 154, 0, 000 155, 0, 000 156, 0, 000 157, 0, 000 158, 0, 000 159, 0, 000 160, 0, 000 161, 0, 000 162, 0, 000 163, 0, 000 164, 0, 000 165, 0, 000 166, 0, 000 167, 1, 000 168, 0, 000 169, 0, 000 170, 0, 000 171, 0, 000 172, 0, 000 173, 0, 000 174, 0, 000 175, 0, 000 176, 0, 000 177, 0, 000 178, 0, 000 179, 0, 000 180, 0, 000 181, 0, 000 182, 0, 000 183, 0, 000 184, 0, 000 185, 0, 000 186, 0, 000 187, 0, 000 188, 0, 000 189, 0, 000 190, 0, 000 191, 0, 000 192, 0, 000 193, 0, 000 194, 0, 000 195, 0, 000 196, 0, 000 197, 0, 000 198, 0, 000 199, 0, 000 200, 0, 000 201, 0, 000 202, 0, 000 203, 0, 000 204, 0, 000 205, 0, 000 206, 0, 000 207, 0, 000 208, 0, 000 209, 0, 000 210, 0, 000 211, 0, 000 212, 0, 000 213, 0, 000 214, 2, 000 215, 0, 000 216, 0, 000 217, 0, 000 218, 1, 000 219, 0, 000 220, 0, 000 221, 0, 000 222, 0, 000 223, 0, 000 224, 2, 000 225, 0, 000 226, 0, 000 227, 0, 000 228, 0, 000 229, 0, 000 230, 0, 000 231, 0, 000 232, 0, 000 233, 0, 000 234, 0, 000 235, 0, 000 236, 0, 000 237, 0, 000 238, 0, 000 239, 0, 000 240, 0, 000 241, 0, 000 242, 0, 000 243, 0, 000 244, 0, 000 245, 0, 000 246, 0, 000 247, 0, 000 248, 0, 000 249, 0, 000 250, 0, 000 251, 2, 000 252, 0, 000 253, 0, 000 254, 0, 000 255, 0, 000 ==Octave script for analysis & plotting== {{SJK comment|label=01:21, 22 October 2007 (CDT)|comment=I had never heard of Octave before, so found [http://en.wikipedia.org/wiki/GNU_Octave a description on wikipedia]. Are you happy with it? Is it easy to use if you don't know matlab? In any case, thanks for posting your analysis code! I hope to have some time to check it out...}} chop off the first ten lines of the data files before use rename variable and filenames as necessary. Probably only needs minor tweeks so that it can run in matlab. <pre><nowiki>#octave #a sort of diary of commands to automate the data processing day to day #some of octave's functions do not work in matlab,and vice #versa. Some functions may work, but not in the same way #Most things work, though. #Tomas Mondragon load LAB3_D10.ASC; #The load function is intended load LAB3_D20.ASC; #to read files saved by octave. load LAB3_D40.ASC; #Load can also read .mat files, load LAB3_D80.ASC; #but only versions saved by matlab load LAB3_D100.ASC; #version 4. It can also read text files. load LAB3_D200.ASC; #if no variable name info is in the file load LAB3_D400.ASC; #it names the variable after the file name load LAB3_D800.ASC; load LAB3_D1S.ASC; load LAB3_D10S.ASC; dwell10ms=LAB3_D10(:,2); #load put what was on LAB3_D10.ASC into the dwell20ms=LAB3_D20(:,2); #variable LAB3_D10. I only care about the second dwell40ms=LAB3_D40(:,2); #column of the data, so here I extract it to an dwell80ms=LAB3_D80(:,2); #appropriately named variable. dwell100ms=LAB3_D100(:,2); dwell200ms=LAB3_D200(:,2); #The first column of LAB3_D10 is the channel number dwell400ms=LAB3_D400(:,2); #but a more appropriate name would be the bin index. dwell800ms=LAB3_D800(:,2); #The second column is a count of how many events fell dwell1s=LAB3_D1S(:,2); #into the bin. The third column isn't important for this dwell10s=LAB3_D10S(:,2); #experiment, but knowing what it is will allow one to take #advantage PCA3's region of interest feature. It just marks #where one has marked ROI's. for example, 4 indicates the bin or channel #lies within ROI 4 #idea:use max(dwell10s) as max bin for all so grapfh are same x scale #[y,x]=hist(data,bincenters) is a a function that sets up bins whose values are centered #at the values given by the vector bincenter and counts the number of times the values in #data fall into each of the bins. y contains the frequncy counts and x contains the #corresponding bin index. bar(x,y) will plot the histogram of data. In general, x=bincenters, #so one can shorten [y,x]=hist(data,bincenters) to y=hist(data,bincenters) and use #bar(bincenters,y) to plot the same thing. bincenters=0:max(dwell10s); freq10ms=hist(dwell10ms,bincenters); freq20ms=hist(dwell20ms,bincenters); freq40ms=hist(dwell40ms,bincenters); freq80ms=hist(dwell80ms,bincenters); freq100ms=hist(dwell100ms,bincenters); freq200ms=hist(dwell200ms,bincenters); freq400ms=hist(dwell400ms,bincenters); freq800ms=hist(dwell800ms,bincenters); freq1s=hist(dwell1s,bincenters); freq10s=hist(dwell10s,bincenters); #plots. press any key to move to next plot bar(bincenters,freq10ms) title("frequency counts for dwell time=10ms") xlabel("number of events occuring during dwell time") ylabel("frequency count") pause replot bar(bincenters,freq20ms) title("frequency counts for dwell time=20ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq40ms) title("frequency counts for dwell time=40ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq80ms) title("frequency counts for dwell time=80ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq100ms) title("frequency counts for dwell time=100ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq200ms) title("frequency counts for dwell time=200ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq400ms) title("frequency counts for dwell time=400ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq800ms) title("frequency counts for dwell time=800ms") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq1s) title("frequency counts for dwell time=1s") %xlabel("number of events occuring during dwell time") %ylabel("frequency count") pause replot bar(bincenters,freq10s) title("frequency counts for dwell time=10s") %xlabel("number of events occuring during dwell time") %ylabel("frequency count")

## Compilation of plots

The plot that the script above produced with the data I obtained are shown in sequence below. As the dwell time increases, the most often occurring event count increases and the frequency vs. event count plots drift from something resembling a poisson distibution of a rarely occuring event to a the poisson distribution of a more common event, which resembles a gaussian.**I should point out that something interesting happened while we we counting events with a dwell of 200 ms. Our equipment recorded one instance where 27 events happened in that small dwell time. The mode of the data for dwell time=200ms was 0 events, and were were rarely getting counts more than or equal to 5.**

^{SJK 01:40, 22 October 2007 (CDT)}

^{SJK 01:27, 22 October 2007 (CDT)}In Dr. Gold's lab manual, the poisson distribution is a model for the results of experiments that count random events that occur at a definite average rate and the frequency that one should expect to get a certain count number. If the expected average count is **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lambda}**
, the probability that one will obtain the result of **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle k}**
after performing the counting experiment is

**Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle f(k;\lambda)=\frac{\lambda^k e^{-\lambda}}{k!}}**

So, to fit my data, I will have to normalize my data and find a suitable **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lambda}**
for each data set.

First off, normalize. If the frequency count of an event count **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle k}**
is **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle x_k}**
, find some normalizing constant **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle N}**
so that **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \sum_{k=\operatorname{min}\ k}^{\operatorname{max}\ k} \frac{x_k}{N}=1}**

Then, find **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lambda}**
such that**Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \sum_{k=\operatorname{min}\ k}^{\operatorname{max}\ k}\left(f(k,\lambda)-\frac{x_k}{N} \right)^2}**
is a minimum

Duurrrrr... **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle N=256}**
because 256 tests were performed each time.

^{SJK 01:38, 22 October 2007 (CDT)}Through an iterative process, I determine

- 10ms,0.0261205
- 20ms,0.0736898
- 40ms,0.185892
- 80ms,0.457154
- 100ms,0.468385
- 200ms,0.937453
- 400ms,2.58578
- 800ms,5.74562
- 1s,7.27233
- 10s,73.9022

^{SJK 01:44, 22 October 2007 (CDT)}how good are these fits, since I decided to stop at 6 sig figs (quite arbitrarily). I suppose I shall quantify this by taking the average of how far off the actual data is from the fit.

I think the formula is **Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle Error=\frac{\sqrt{\sum_{k=\operatorname{min}\ k}^{\operatorname{max}\ k}\left(f(k,\lambda)-\frac{x_k}{N} \right)^2}}{\sqrt{N}\sqrt{N-1}}}**

- 10ms, 0.0261205, 5.45905*10^-6
- 20ms, 0.0736898, 1.19310*10^-4
- 40ms, 0.185892, 3.28259*10^-4
- 80ms, 0.457154, 5.95464*10^-4
- 100ms, 0.468385, 3.15888*10^-4
- 200ms, 0.937453, 5.23153*10^-4
- 400ms, 2.58578, 5.22450*10^-4
- 800ms, 5.74562, 2.97039*10^-4
- 1s, 7.27233, 2.59775*10^-4
- 10s, 73.9022, 2.96150*10^-4

**Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \frac{\lambda}{dwell time}=some constant}**

A plot of ^{SJK 01:38, 22 October 2007 (CDT)}

slope=7.39233+/-0.00003 intercept= -0.048099+/-0.000005 cov(m,b)=0.000000 correlation=0.999983 point error estimate=0.231612 chisq/ndf=265341So, with our equipment set up the way it was (sorry, no data on this, oops!) we were observing events that occured at an average rate of 7.39 events per second.