Building a polarimeter

Thanks Aga. I was kind of thinking the same thing, but so many of these example circuits use 10Mohm, and even gigaohms. I was looking at that and scratching my head after I had read up on signal noise. I believe the LTC 1050 has a max gain of 20db also. So I am sure I have been wayyyyy over-loading it. This would also explain the clean signal with the extra capacitance.

I think I will try a transimpedance(current->voltage) which leads to a classic non-inverting voltage amplifier. I believe with 440kOhm resistance I was seeing 0-0.125V signals. So a R1/R2 = 40ish (or 20ish to be safe) should be fine. Again that's two stages with pretty big gain and most people say that to put the noisiest/largest gain stage as the first one. We'll see. I'll attempt it using two LTC1050's. It just makes the most sense right now.

[Edited on 22-5-2014 by smaerd]

Update- Ran my first trial with a dual stage amplification. Not bad. I mean very noisey but this seems like it will be easier to hone in on. As it is noise, not wild oscillation(okay some oscillation but it looks like there are two wave-forms not an infinite sweep).

Think the next step is actual shielding(not laying down foil), and transferring to prototype board after a few more simple tests. Then fine tuning capacitors/resistors as best I can. Also, Aga I took your advice. Drank a few beers for science. Well, the first one was to shield the motor , the second was well just incase I cut the can wrong, etc.



[Edited on 23-5-2014 by smaerd]

[Edited on 23-5-2014 by smaerd]

Are you sure? I just started getting great data.

The gain is nearly perfect(~0-~2.0V), the oscillations are gone. Just some stray noise. Need to fine tune this and see where this can be coming from. Motor is shielded. Should shield the audio jack plug next to see if that will improve anything. I don't know if I need an RF choke or not. Not sure if the analog pins have a common ground with the digital on the leonardo, I'll have to check to be sure. I'm thinking that a teeny tiny bit more tuning with capacitance and this thing can go onto some perf board!



[Edited on 23-5-2014 by smaerd]

[Edited on 23-5-2014 by smaerd]

[Edited on 23-5-2014 by smaerd]

Forgot all about the ADC... Well I've shielded damn near everything I can think of. I need to take this to perf-board. Alot of this could be induced by stray capacitance of the ridiculous jumper wires I am using. Or capacitance of the spinning audio-jack(worst case scenario) I am using this type,
.

Honestly every connection has 2-3 inches more wire then is necessary. Also there is the capacitance of the bread-board itself, and resistor prongs. It's also a lot harder to shield a bread-board(can't wrap it in foil without risking shorts). The PWM motor driver bread-board running with 12V is maybe 3 inches away from the detector board as well. Tried shielding it but it's a tangly mess. Need to put that on perf board as well and shield it. Once it's on perf, I should be able to tune it. I'll wire wrap the capacitors until I get where I need to be.

Well one thing I did realize with this project is, the mechanics/code and circuit could be used to build a UV or at least a VIS spectrophotometer(~200$ spectrophotometer that isn't a black box). Rather then rotate a polarizing element, rotate a grating element. So once I figure this out that may be an interesting follow up project. Or maybe someone else will take the lead using the same kind of idea. I'll definitely be making it all public domain once finished.

[Edited on 23-5-2014 by smaerd]

It's not a stupid question but I am not sure what you mean if I see the light? Yes the light is visible on the detector to me and to the detector, but I try not too peak while the thing is running. I have not tested it with a cell yet. I am currently working on an algorithm to position the analyzing polarizer to a minimum. Then as soon as that is done, I will be able too implement the pre-written measure command to take a measurement(series of measurements), and observe the data. Which the soft-ware will then give the appropriate information useful for chemical analysis. So essentially once this noise is gone. An hour of programming and tidying up and this should be a completed project. Wellll, I still need to buy a cell and build a little mount for it, for testing but that will happen when the time comes... Or I'll come up with plans to build one for an affordable price...

Also long over-due are the instrument photographs. Had to borrow someone elses camera as mine stopped working. As you can see the laser circuit is currently disconnected from the arduino board for now and running off two triple AA's. Kind of a nuissance but I am trying to eliminate all the variables I can while working out this portion of the circuit.

Edit - Please don't judge too harshly on the choice of beer. It was what was in the fridge



[Edited on 23-5-2014 by smaerd]

[Edited on 23-5-2014 by smaerd]

Awesome! Never heard of a back scatter polarimeter. I'd love to hear about your progress/design. Edit - Oh wow! http://pubs.acs.org/doi/abs/10.1021/ac951169b

Polarimetry in Capillary Dimensions
Darryl J. Bornhop * and Joseph Hankins
Anal. Chem., 1996, 68 (10), pp 1677–1684

Yea I just read an article by bob pease "What is all this common ground noise anyways?". Was pretty enlightening. I also remember from my physics course about what Mr. Faraday and Mr. Maxwell said pertaining to loops of wire in the presence of changing magnetic fields . I also realized how bread-boards are almost perfect for creating those loops... I'll have to read up on good lay-outs to avoid this when I transfer the thing to perf. board. Also the effect of the photodiode and the circuit desperately wanting to pull current from all over has been a bit mind-blowing to me. I'd love to see the thermodynamic or E&M theory explaining this more fully.

[Edited on 23-5-2014 by smaerd]

Very interesting. I assume a mirror will be behind the sample? I'm a little confused by the optical diagram but hell it's ASCII hahaha. Think I get the jist. Well I fine tuned my code and found the actual number of pulses per revolution. Made a mathematical error in my early theoretical calculations that unfortunately stuck with me until now.

Anyways the harmonic regression is now 'dead-on'. So I can move forward a bit. By tonight I will hopefully have the majority of the soft-ware written. The analysis for the measurement of the sample will likely require a fourrier transform which is something I kind of over-looked until now that it's almost on the to do list.



[Edited on 24-5-2014 by smaerd]

Ooo that looks highly adaptable aga. I am using JAVA simply because it's a quick development language. Not quick performance-wise, but I've had no issues yet.

Well happy to update. I worked out the orienting algorithm, and the measuring algorithm(which was cake). Now I can officially say, noise aside, I have constructed an automatic polarimeter!

To do list:
- Obtain a sample cell
- To transfer circuits to perf board and shield (should handle the noise)
- Fine tune some of the algorithms once I have non-noise results
- Have the soft-ware to plot the results(already have it set up have just been lazy), and find maxima's.
- Test with some known compounds and get some real results.

It's been a long journey! I would apologize for spamming the crap out of this thread with noisey data and my thoughts but, I'm not exactly sorry.

The following image is a 180* rotation of the analyzer to find/interpolate the nearest minimum intensity value on the analyzer to rotate too.


The following image is what happens once the minimum is found and the measurement button is pressed. The analyzer rotates generally about 90* away from the darkest point(with the sample in instrument) to obtain a 'semiconstant' angular velocity. Once it hits the minimum the data collection begins. Once it goes 360.0* from the minimum the data collection ceases. With nothing in the sample compartment, clearly two peaks are the result. Notice they are ~ equal in height now that the laser is aligned.


Interestingly the noise on the second peak is more severe. I believe this may be attributed to the antennae effect. The longer the gain circuit operates, the more it wants to induct/pull from the fields in the air. We'll see.

Start(orienting) to finish(measurement) it takes around 1 minute. It might be fun to write some kinetic experiment handling in the soft-ware. A fun test would be to do the classic mutorotation of glucose? Or maybe it's sucrose I forget, my brain is fried. Then compare results. Would be really nice not having to touch a thing either.

Drinking a beer to celebrate. Well actually to tone down the ridiculous concentration of caffiene and theobromine coarsing through my body. Irregardless, very happy!

@Aga - Thanks for following this with me. I'd love to see your back-scatter polarimeter set up. It's an interesting concept. I will have to think about whether the polarization will increase or not after reflection. Probably be more fun to experiment with it though. Never know what you might find.

[Edited on 25-5-2014 by smaerd]

[Edited on 25-5-2014 by smaerd]

A little upset. Went from bread board to perfboard in hopes of getting a cleaner signal. Instead I somehow have an incredibly awful one. I'm not sure what is going wrong just yet. A little worried I may have somehow fried one of my op-amps while soldering. Might save troubleshooting until tomarrow as this has been a real disappointment and I've triple checked the circuit.



Edit- I cleaned up the signal a little bit, but there is no or very small amplification. No longer are they clean sinuisoids, and the noise is just as bad if not worse than before. Ughhh, might of been better on bread-board.


Bought some DIP 8 sockets. I definitely fried ANOTHER op-amp hahahaha, this time by soldering. Ordered some different ones that should be good performance-wise. So it will be back to bread-boarding then protoboarding in 4 or so days... Soon as this circuit is done though, the instrument is finished. So painful to be so close and be stuck waiting.

[Edited on 30-5-2014 by smaerd]

Well I was using a 100-120 watt iron, with a copper tip(original tip burned out so I replaced it with some 12 AWG solid core copper wire). Definitely burnt and melted some of the PCB along the way . Try not to judge too harshly by my poor soldering job this was the second circuit I've ever put on protoboard. I tried to heat the PCB more then the pin and apply little blobs of solder but it didn't work as well as I'd of liked it too. The iron I have isn't made for these kinds of tight connections either. I think the solder I am using might be bogus as well, it's "cold heat" solder... Not even sure where I got it from.

Would you prefer to have connections labeled because it looks pretty confusing to me?

The conglomerate of soldered wires leading to the negative supply is something I was doing to test whether the issue was related too my power supply/decoupling portion of the circuit(rebuilt it on another part of the board). Power supply was functioning fine. I tested around kind of quickly with a multimeter around the op-amp stages and I believe it was the transimpedance stage that appeared wonky. Was a few days ago so I can't remember exactly what seemed wrong with it(needed a break from it).

Also on the back of the board you'll notice some scratch marks between lines going to the IC. I did that with a razor because there appeared to be a small short in a few areas. I unfortunately do not have desoldering whick or a desoldering sucker thinking about improvising one, but might just go with soldering in sockets then putting in the chips. The LTC1050 has this pin called "EXT CLOCK INPUT" or something. I have no idea what it does and can't find technical information about it, but I think I may have shorted it at one point with this circuit as well. The last time I did that on bread board it fried the IC(goo leaked out of it?).





[Edited on 31-5-2014 by smaerd]

[Edited on 31-5-2014 by smaerd]

[Edited on 31-5-2014 by smaerd]

Thanks for letting me know about that pin. I mean I assumed that was it's function, just wasn't sure how it would respond to say 5V essentially D.C. being thrown at it or if it would need resetting . Just going to start fresh instead. The LTC1050's are great little op-amps but I thought about it and a lot of the performance I need could be handled with some cheaper more ubiquitous components. The non-inverting voltage gain stage, really didn't need to be an LTC1050, at all... Think a TL082 will do fine there. We'll see how the parts I spec'd out will do. Originally I wasn't fluent enough to actually decide on the chips, now I'm more confident in my decisions.

Yea pretty much a blow-torch hahaha. Thing can melt solder in 2-3 seconds which is way too much for a PCB or a sensitive IC. I'm going to go buy a cheapy 50watt I think just for future projects, not everything I do has to be improvised. Guess it's how I was raised. Wish I would of known about those DIP-8 sockets for protoboarding before doing this, live and learn.

Nice let me know how you like the Uno. I'm using a Leonardo. I'm okay on programming, well it was my first time doing anything with a microcontroller but I kind of have the hang of it. Spent many years writing code growing up, so that helped, and also helped with writing the front-end. Kind of crazy how you never really forget that kind of stuff. Arduino's are nice, as they are kind of higher-level("sketches") but there is access to the lower level stuff if you really want to dive into it. I definitely use the lower level digital read commands for speed (not that it's necessary but it makes me feel safer). Still need to implement my ADC stabilizing stuff for accurate readings but the circuit comes first before fiddling there. I was actually considering switching to a rasberry pi or beagle bone black just so I could really rip my motor and get all the data I wanted quickly. Even store said data, rather then relying on it passing through the serial pipe. Ultimately though, this will work fine.

If you plan on doing serial communication and get lost let me know. Big hint for me was downloading the arduino source-code and seeing how they handled everything (gotta love open-source, no need to break out the decompiler ). I have some pretty decent integer passing algorithms and things(not that it's a difficult problem to solve, break them into 2 byte chunks and just pass them down). I can get you the source code I have to build off of, that's what community is for. It's in JAVA though, which I know most real programmers find horrendous, but the idea's are the same. I haven't cleaned up my code much yet, that's kind of a finishing touch type of thing. Function comes first.

[Edited on 31-5-2014 by smaerd]

[Edited on 31-5-2014 by smaerd]

So I finally had some time to replace my old op-amps, buy some 1% resistors, etc. I never got to tell ya'll, I was able to remove the noise from the measurments! All I had to do was abandon the audiojack and limit some of the capacitance by using 22awg bare solid core wire on the bread board.

The only thing that's been stifling the project now is simply aligning the detector and sample cell. I am working on a way to do this with craft foam that I did fiberglass and bondo over. I'll let you all know if I get it to work out.

Anyways here's a screenshot for the data of an alignment run. Notice there's no stray dots. Also notice it's not a clean sinuisoid because my source and detector are not parallel. But no more noise!



edit - if anyone has any nice DIY ideas for creating a sample cell holder and photodetector holder I'd love to hear them. I'm still worried this foam idea won't work out. It's sitting on foam now and still a pain to line up.

Can't wait to put this idea to rest after two years of off and on working between semesters.

[Edited on 10-5-2015 by smaerd]

So.... I finally have the signal working out, yahoo right? I fixed all of my soft-ware bugs, great. I ran my first trial. And it doesn't look as though I am even polarizing the light lol.

So I did a blank orientation run, and a blank measurement run (left and right images below)


Looks like my motor positioning algorithm is a bit off. It looks like I've started taking measurements too late to catch the first sinuisoid at it's minima. The maxima are at about 270* and 90* (have to add the offset of ~25*). Which means physically and electronically everything is working okay, despite the imperfect sine data. (not sure why this is, things are aligned pretty well, might be too much feedback capacitance)

Then I set up to do another run this time with a sample.
I ran my orientation run (to find min & maxes of a blank cell). Notice that the intensity is quite high, near 900 counts. 87% of the maximum voltage for the microcontroller - amplification success. I'm pretty proud that I was able to work that out without anything other then a 10$ multimeter.


I made a 20% w/v sucrose solution (20g per 100mL) and put it into the sample tray


It's obvious the absorbance has increased, which is a good sign. It doesn't look like the angle of rotation has changed much if at all from what a blank run should be(near 280* and near 100*). Finally conquered some yucky serial transfer code. Now it's just a matter of fine tuning the microcontroller and maybe the amplification circuit.


[Edited on 19-5-2015 by smaerd]

[Edited on 19-5-2015 by smaerd]

Quote: Originally posted by smaerd

if anyone has any nice DIY ideas for creating a sample cell holder and photodetector holder I'd love to hear them. I'm still worried this foam idea won't work out. It's sitting on foam now and still a pain to line up.

Quote: Originally posted by smaerd

So I finally had some time to replace my old op-amps, buy some 1% resistors, etc. I never got to tell ya'll, I was able to remove the noise from the measurments! All I had to do was abandon the audiojack and limit some of the capacitance by using 22awg bare solid core wire on the bread board. The only thing that's been stifling the project now is simply aligning the detector and sample cell. I am working on a way to do this with craft foam that I did fiberglass and bondo over. I'll let you all know if I get it to work out. Anyways here's a screenshot for the data of an alignment run. Notice there's no stray dots. Also notice it's not a clean sinuisoid because my source and detector are not parallel. But no more noise! edit - if anyone has any nice DIY ideas for creating a sample cell holder and photodetector holder I'd love to hear them. I'm still worried this foam idea won't work out. It's sitting on foam now and still a pain to line up. Can't wait to put this idea to rest after two years of off and on working between semesters.

@aga - I'm not tweaking the intensity signal of the photodiode in the soft-ware, I'm tweaking the motor rotation. The issue now is "clipping" of the signal (sine wave hits minimum for a long period of time) and it looks like the sine function extincts more slowly then it should. I'm thinking thats circuit only work unfortunately, but if I buy maybe 3-4 capacitors in the right range I should get better results. I might add some smoothing functions later to the data but I'm keeping it as 'raw' as possible. Then again the signal to noise ratio seems really small so it's probably unnecessary.



Here *pops the hood*. Do you see how the detector is suspended on the aluminum frame(on the right) and how on the left there's the light source. Now I've finaggled around a bit and I have a system worked out with planks of wood on screws so I can adjust the position of those things. I really want a way to align the lightsource and the detector with something more permanent rather then wood. Any ideas would be appreciated.

@Irc - The soft-ware I'm using is soft-ware I've been writing as the project has progressed. It's all JAVA, nothing too indepth and I'm sure a professional soft-ware engineer wouldn't like my approaches/structuring but it works and isn't heinously sloppy. If you need help doing things like this or want some source code to build off of, simply ask, I share code for free and no royalties or whatever.

I'm not exactly willing to pass out my code for the polarimeter yet though until I reach a stable version (IE when I'll post a complete write-up). Otherwise I might lead someone into a dark corner. In the mean time though I can give out snippets or how I approached problems .

[Edited on 20-5-2015 by smaerd]

[Edited on 20-5-2015 by smaerd]

Hmmm, so I had my go with sucrose again after I totally revamped my positioning algorithm. I found out the hard way, my data is not-sinuisoidal enough to do a formal second derivative analysis :/. Kind of a bummer, so I came up with another way to handle my motor. I won't bore you with the details unless you wanna know.

Anyways the positioning algorithm appears to be working wonderfully. Picture on the left is the unoriented analyzer/motor (notice the little tail of the sine function going upwards on the right hand side?). Picture on the right is the oriented polarizer with sucrose solution (notice no tail).




Unfortunately... It looks like my sucrose solution is not polarizing light whatsoever. My peaks are locked in at 90* & 270*(raw data file attached). It probably is polarizing light, just minorly, which I could write a routine to detect these shifts but I want to see something more promising before I write another routine... So I am going to really up the concentration and see if I can get something drastic. 20% was nothing, let's try 60.

I'm really hoping I don't need a specialized substrate for this wavelength.

[Edited on 20-5-2015 by smaerd]

Attachment: 2015-05-20_160802.csv (306kB)
This file has been downloaded 702 times

[Edited on 20-5-2015 by smaerd]

Here I'll outline whats going on. I think you're correct with what you said I just want to be clear as possible because there's a good chance any passerby would be uncertain as well. Especially after the fuss that happened in my DIY rotovap prepublication thread because I didn't take enough pictures lol.



[Edited on 20-5-2015 by smaerd]

[Edited on 20-5-2015 by smaerd]

Thanks for the offer, I don't think I need to change out my motor. I'm getting pretty good positional accuracy here.

So I just tweaked my op-amp circuit. I reduced the gain on the first stage pretty significantly, and found two more balanced resistors (5% sure isn't 5%, someone at QC goofed up on the 220 K ohms I was using). Then I increased the gain of the second stage to compensate. I'm at about 4/10ths of the arduino max signal potential. Thats running on two highly used triple A batterys for the light source. Not bad. Signal looks good, that's really all I care about.

Here's a picture of my current noise situation(zoomed way in). It's acceptable to me, considering the signal is about 100x larger in magnitude.


I toyed with changing the capicatances on the op amp stages, reducing them to 100's of pico farad was a bad call. Lots of oscillations essentially pure noise. I tried 1/10th what the capictance is now, didn't really change the clipping at all. or the band shape.

Anyways the noise looks a little prettier to me than how it was before so I'm gonna keep it this way. If I had an oscilliscope I'd be able to tune this thing more, but this serves it's purpose and seems to work well.I'm leaning more towards the physical allignment being the culprit for the funky band shapes.

I also found a source for a small error in my positioning algorithm. I'm not sure how to overcome it just yet, I think I'll have to hit the drawing board.

[Edited on 21-5-2015 by smaerd]

Give it a shot aga it's really not a major project. The only reason why it's taken me so long is stupid mistakes like using a 100w soldering iron and melting IC's lol and lots of school and other busy life things.

I just fine tuned my firm-ware a bit and I seem to be getting acceptable results. I tightened up my alignment as best as I could so now I'm really not sure why I'm getting those funky band shapes.

I'm trying to think of some good cheap test substrates or an experiment I can perform to test this thing out. All that's really left to do is wrap up my soft-ware and firmware then maybe try an LED again with the new amplification stage. I think I abandoned the LED too soon, but I was frustrated at that point.The nice thing about an LED is that I could compare my results to literature values.

Edit - So I just tried holding one of those super bright LED's I bought a while back about 10cm from my detector. Looks like I can pull a hundred counts out of it without changing my amplification stage, not bad. I am going to try and switch back to an LED design.



[Edited on 21-5-2015 by smaerd]

I was able to get a signal and everything which was great, I realize I could improve the optics of the LED and change my gain and yadda yadda yadda. Then I remembered why I was so happy with the laser diode, its so easy, its point and shoot (thanks bfesser for that suggestion it changed my entire project).



I found a web page which stated that the greater the wavelength of light the less polarized it became by a sample. Which physically makes a good deal of sense. I believe they said at 436nm the polarization can be 2x as much as that of 589nm(http://rudolphresearch.com/products/polarimeters/polarimetry...). I'm not sure if my diode is 650nm or 680nm but regardless it explains the low specific rotation values I was seeing.

So I did some scoping around and 532nm laser diodes are very cheap, will give me a greater polarizing effect then 589nm which may be beneficial (less sample for analysis), and best of all they are in a range which my detector is very sensitive! So I may not get as much clipping or any at the lower light levels. The nice part of this design is I can interchange light sources, so if someone ever produces a 5mW 590nm laser or something I'll snatch one up. In the mean time...

No literature comparisons, but using less sample, and ease of use is good enough reason for me. Besides do I really care about the specific rotation of something, no, I want to use this thing for analysis .

The other funny thing about this is, I can actually use this sucker as a colorimeter from about 400nm to 700nm. So yea it's not a UV-VIS or totally practical but heck I have often wanted a colorimeter anyways. I'm definitely going to modify the sample comparment area in a modular way to incorporate that functionality.
[Edited on 22-5-2015 by smaerd]

[Edited on 22-5-2015 by smaerd]

So I built a farraday cage around my house and implemented ferrite chokes on all my lines, balanced my circuit with handfulls of gimmick capicitors, made a new ADC for the arduino. Okay those are all lies to make aga giggle.

But I did get rid of all of ADC noise. I borrowed an FFT library (JTransforms) and wrote a quicky high-pass filter into my software. Now I can finally fine tune the positioning algorithm. The second derivative tests should be reliable now. The best part of this type of filter is simply that none of my band shapes are shifted, and the amplitudes remains nearly the same. All it does is rips high frequencies out of the spectra.You'll notice that the units on the Y-axis after the inverse transform are scaled on the order of 100,000. Who cares? Absorbance units are arbitrary anyways.

Check these signals out,



[Edited on 24-5-2015 by smaerd]

By doing this I was able to get my motor positioning resolution down to a factor of 10 with an unoptimized algorithm. If I can tune this one more time I can see atleast a factor of 5-10 more resolution then my soft-ware will be complete aside from frilly things.

[Edited on 24-5-2015 by smaerd]

I just started reading this thread but couldn't resist jumping ahead to the last page.

Man, I can hear the gears of improvement (not the motor drive gear) turning all the way across the internet ocean. Seeing your graphs, it looks like you achieved smooth, constant rotation of the rotating polarizer. That's what I call a sine wave!

BTW, did you mean to say you implemented a low-pass filter or did I miss something?

Oh gosh you're absolutely right m1tanker, yes I meant a low-pass filter not a high-pass filter. I used a "brick-wall" algorithm which basically goes FFT-> Remove frequencies outside of threshold(turn them to 0) ->inverse FFT . So the filter wasn't electronic it was soft-ware, because I speculated that the noise I was seeing was ADC noise. I deduced this by chucking the arduino ADC clock to 1MHz and noticing some distinct changes in the spectra/noise appearance. The brick wall is not as good as masking, but my data is essentially one sinuisoid and the rest being highfrequency noise so the brick wall is juuuust fine.

Before the FFT I was seeing 1-7* error in positioning the polarizer. Not good.

Now I'm just tuning the "peak finding" algorithm. After the FFT I was getting lots of 0.081* errors (off by ~3 motor encoder counts), then I saw some more 0.50* errors for the positioning (made a few too many assumptions in my routine). So I gotta come up with something more reliable but so far I can safely say I am at 1* accuracy at least. My goal was a consistent error of ~0.05* (1-2 counts off from predicting the peak). If I can hit that then maybe I'll try running in quadrature and getting a slightly larger gear and then I could hit 0.01*.

Also once I swap out the laser I should no longer be seeing the clipping at the bottom of the sine waves (fingers crossed).

Thanks for dropping by .

You've gone and done it now smaerd.

You made me build a polarimeter.

It looks like a really great start aga. If you want my amplifcation stage circuit diagram or anything else let me know .

Yea 90% of my battle has been just setting up the physical components, so the rest should be smooth sailing for you. I really like how you used a mirror to get things into place I didn't think about that, but its a lot easier to adjust a mirror then move a mount on wood.

Quote: Originally posted by smaerd

Also once I swap out the laser I should no longer be seeing the clipping at the bottom of the sine waves (fingers crossed).

Sorry smeard, I thought the graph offset was off and my brain sort of auto-completed the sine wave. I don't want to be the guy that asks a thousand questions that have already been answered or covered upthread so I'll refrain until I get through it.

The important thing is that aside from tweaking, you have the hardware and logic throwing raw data at your computer. From there, it's [almost] all math!

OK, one quick question.. how do you account for the source polarization when you switch to a laser source?

It was a surprise to see so little variation on the detector !

I had assumed that the laser would saturate the detector, so chose a pretty insensitive one.

Out of a range of 1024 points, i get a variation of just 10 !
Time to try a new detector & op-amps i guess.

Also need to replace a screw, as one 'dip' is the screw blocking the laser ...

Upping the amplification in software gives these results :-

Nice work there Aga! I can see a sinuisoid emerging from there. I think some of your weird band shape might have to do with the way the polarizing element is rotated.

Yea also most solar cells don't have a linear response for illumination vs voltage right? So you'll probably need either a massive resistor or a TIA amplification stage like I did.


---
Also, on my front, I made some huge progress. I'm getting my reproducibility for motor positioning to be between 0.027-0.081*. So I have successfully nailed it down to ~+/-0.1*. How did I do it?

Well I examined the frequency domain near 0 Hz. I noticed I had a big peak at nearly 0 (slightly off), a smaller one (good makes a wave form), then I had a little funky ripple which was actually assymetric with the negative portion of the domain(not shown due to the half FFT transform I'm using here, but in the full FFT it's there).


So what did I do? Trimmed off the assymetric wave (the portion highlighted in blue) form via my low pass filter. What's the result? I'm now commonly off by 1 encoder pulse (which I can account for) sometimes slightly more or slightly less. Now I haven't done a sinuisoidal regression, but I doubt wave forms get much better then that with a 10bit ADC. So why the huge increase in reproducibility and precision/accuracy, well, my algorithms can finally work on the nice data, the sole problem was the nonideality data (I had to rule out everything else).

No more clipping! I believe this band is lower in frequency as it represents either laser polarization error, or imperfect alignment(maybe both).



It sort of begs the question, is it okay to do this type of data modification. I thought about it all morning because last night I stated it would be data manipulation. Here's the thing, I'm not changing the frequencies of interest in the slightest bit (well in the 11th or 12th digit yes but that is beyond the resolution of the instrument). I am simply removing a constant interferance wave-form and noise from the frequency of interest. It turns out, go figure, that my data is a clean sinuisoid after that, no surprise.

It feels good to successfully surpass a 500$ instrument . Now it's just a matter of fine tuning a few more things.

[Edited on 25-5-2015 by smaerd]

Attachment: So Clean -20150525_121733.csv (362kB)
This file has been downloaded 818 times

[Edited on 25-5-2015 by smaerd]

Quote: Originally posted by smaerd

It sort of begs the question, is it okay to do this type of data modification. I thought about it all morning because last night I stated it would be data manipulation. Here's the thing, I'm not changing the frequencies of interest in the slightest bit (well in the 11th or 12th digit yes but that is beyond the resolution of the instrument). I am simply removing a constant interferance wave-form and noise from the frequency of interest. It turns out, go figure, that my data is a clean sinuisoid after that, no surprise. It feels good to successfully surpass a 500$ instrument . Now it's just a matter of fine tuning a few more things. [Edited on 25-5-2015 by smaerd]

So I did some work on this today. First things first. Thank you M1Tanker. You were right the red laser pointer does have a significant source polarization. I removed a polarizing film from the optical path and swapped my detector for the source as suggested. Now I have clean sinuisoids without filtering.

So I added a constant voltage power supply for the laser pointer, so glad I did, now my FFT filter has a constant setting!



Anyways, now I took some results as the instrument stood without fine tuning the soft-ware for the new alignment. It's pretty buggy still, but now I have eliminated two or three huge issues. So again thank your M1Tanker. I can see polarization!



Here are the results:
Without a sample here are the observed rotations: 0.52*, -0.60*,0.22*,-0.27*(Average: 0.033, STDEV = 0.5)
With a 20% sucrose solution: : +7.83*, +9.67*, +9.36*, +8.08*, (Average: 8.74, STDEV = 0.9)

The mean value gives me a specific rotation of 43.7 (+/-4.5)*, which is reasonable.

The instrument is obviously not consistent but now that I have a consistent sinuisoid I can do curve fitting rather then my calculus based approaches to finding peak locations.

As suspected the variance of the orientation is 2X that of measurements, because the routine is run twice to take a measurement. So it is my algorithm that is off.

[Edited on 31-5-2015 by smaerd]

Edit - also I got the green laser pointer but when I shorted the switch on the circuit and subjected it to the 3.3V source. I'd subjectively say it's 100-200 times brighter then the red laser, but knowing the human eye is ~5-10x more sensitive to green then red, this is probably a 50mW laser. It too is polarized. It is bright enough that I would be concerned for my eyes if it were to be shined there. I'm afraid to even try it on my amplification circuit, it would likely saturate it and I'd need to use a 50kOhm trimmer pot on the second stage, too finicky for my blood knowing how the ideal FFT filter is.

[Edited on 31-5-2015 by smaerd]

Quote: Originally posted by smaerd

So I did some work on this today. First things first. Thank you M1Tanker. You were right the red laser pointer does have a significant source polarization. I removed a polarizing film from the optical path and swapped my detector for the source as suggested. Now I have clean sinuisoids without filtering. So I added a constant voltage power supply for the laser pointer, so glad I did, now my FFT filter has a constant setting! Anyways, now I took some results as the instrument stood without fine tuning the soft-ware for the new alignment. It's pretty buggy still, but now I have eliminated two or three huge issues. So again thank your M1Tanker. I can see polarization! Here are the results: Without a sample here are the observed rotations: 0.52*, -0.60*,0.22*,-0.27*(Average: 0.033, STDEV = 0.5) With a 20% sucrose solution: : +7.83*, +9.67*, +9.36*, +8.08*, (Average: 8.74, STDEV = 0.9) The mean value gives me a specific rotation of 43.7 (+/-4.5)*, which is reasonable. The instrument is obviously not consistent but now that I have a consistent sinuisoid I can do curve fitting rather then my calculus based approaches to finding peak locations. As suspected the variance of the orientation is 2X that of measurements, because the routine is run twice to take a measurement. So it is my algorithm that is off. [Edited on 31-5-2015 by smaerd] Edit - also I got the green laser pointer but when I shorted the switch on the circuit and subjected it to the 3.3V source. I'd subjectively say it's 100-200 times brighter then the red laser, but knowing the human eye is ~5-10x more sensitive to green then red, this is probably a 50mW laser. It too is polarized. It is bright enough that I would be concerned for my eyes if it were to be shined there. I'm afraid to even try it on my amplification circuit, it would likely saturate it and I'd need to use a 50kOhm trimmer pot on the second stage, too finicky for my blood knowing how the ideal FFT filter is. [Edited on 31-5-2015 by smaerd]

Actually I don't think I ever elaborated on this piece of information so these are great questions.

1. For a complete polarizer rotation there are 13,132 measurements (weird number I know, but it was experimentally found). So 360*/13132 = 0.027* per encoder count.I can actually double the encoder count number by running in quadrature (but it isn't worth it right now), or by expanding the gear size/tooth count.

2. Here's how the data is transferred/dealt with currently.

Motor encoder detects position change -> photodiode take a measurement (with-in 20μs) -> Data is sent over USB to soft-ware -> software stores information until analysis is completed.
->Soft-ware then FFT filters -> Calculates maxima locations -> Phase shift -> interpolates the next minima to rotate too -> etc

Scans can take from 20s-120s depending on how fast I PWM the motor. I'm preferring 40s scans just for 'safety' even though I had no difference in results with 30s scans.

3. The transferred value is based on a 1024 count (no decimals 0-1023) which the ADC reads as a voltage (0-5V). So all real values. There is no packing the value is recorded as an integer(2bytes), individual bytes are chucked sequentially down the serial pipe.

I'm not manipulating the data on the fly, I could by creating another thread for the application, but I really don't like multi-threaded applications for stability purposes.

Sinuisoid amplitude - I had never heard of a zero crossing algorithm before. Funnily that was one approach I considered, monitor the first derivative for greatest and smallest changes. That was a portion of the algorithm I was using which gave me 0-3 encoder count errors (0-0.08* off).

I think the best method would be to go back to a harmonic regression algorithm, because the 'artificial' sinuisoid will have an absolute maximum rather then an imperfect plateau. Then again, I'm open to suggestions .

Green laser - That sounds like a good idea, but remember I removed the stationary polarizer . It seemed like when I had the stationary polarizer and a polarized light source I was not able to get polarization measurements of the sample cell. It also gave me a 'biased'/off-set waveform for a result. I found that counter intuitive but I am going to accept it for now as that was the only change of the instrument/soft-ware.

With batteries the source was not as ridiculously intense, but I think the intensity is limited by current not voltage (my supply can offer 1A). I didn't analyze the driver circuit too much other then how to short the switch(which was trickier then one might assume). I could try it once I stabilize the algorithm but for now I think I am happy with the Red laser, even though the green laser may give an extra significant decimal for some samples. I could also implement a filter to reduce it's intensity, which funnily enough sounds easier then current regulating the circuit.

Linux -
Yes I am running a linux operating system . My USB ports are ACM0-5, but the soft-ware includes COM and whatever the hell Mac's use.

[Edited on 2-6-2015 by smaerd]

Smeard, I'm confused as to how you derive the imaginary ( i or j ) component of the signal when as far as I can tell, you don't have complex samples to begin with. Are you applying a Hilbert transform or something?

Again, if your amplitude measurements were relative to zero, it'd be an enormous shoe in for measuring the zero-crossing points and hence, your phase shift. The accuracy would be limited only by the usual factors like sample rate, sample depth, mechanical jitter, electrical noise, etc... Rather than trying to measure the peaks where you have an ocean of similar-valued amplitudes, you'd be looking at a sharp transition through the zero 'point'. The trick to knowing if it's a positive or negative-going zero crossing is to compare the current sample with the previous one(s). The zero point doesn't necessarily have to be zero-valued. My memory fails me ATM with the terminology, sorry.

Anyway, no brain-busting calculus or trig needed to find zero crossings and it's incredibly easy on resources.

New film fitted, so now there's an actual disc of un-scratched film, and a static piece as well.

The results with no test tube in place are a bit random, due (i think) to the direct laser light saturating everything.

With an empty test tube i now get this on the arduino's TFT shield :-



Edit:

I initially got 4 peaks, then realised that only 180* rotation really counts.

[Edited on 5-6-2015 by aga]

Yea aga if that's what you want then thats good enough for general purposes . I just want at most 0.10* or ideally 0.05*.

Back to your center of gravity thing. I think that could work. Assume your sine function follows the general form of a sine function(Amplitude * Sin(inside terms) + Amplitude). What it requires is that there is only 1 peak or location above the offset or the + amplitude term. So you must carefully select half of the phase(90*) of the data in that way. Other-wise you're likely going to be finding the point of inflection between the peak and the valley.

I tried going through your excel sheet but I'm a little confused by it. I see some minor errors in the D6 & D7 cells (not the right formula?) and in the G7-G34 cells (no dividing by ten there?). Also why divide by ten, unless that's the moving average script inwhich case ignore this comment.

One way to find such a value would be to use your smoothed function. Find the set of points that are greater then the + amplitude term. Then implement the CoG algorithm there. I could be wrong but I think in this case you might have to add a subtraction term in the for next loop to account for any offset of those values. IE: if your peaks start at say 100 counts you might have to subtract 100 from the I * term so it would be (I-100) * samples. Also this script will not work if your peak shape is split meaning you have half a sine peak then the valley then the other half of the sine peak.

Why not try the zero crossing algorithm, it's really really easy! Here's the simple zero cross I wrote