version 1.5.0.0 (4.17 KB) by
Carsten Killer

Fourier-based reconstruction of an unknown radial distribution assuming cylindrical symmetry.

The reconstruction of the radial density distribution of a cylindrically symmetric object is a common task in different area of physics (e.g. plasma physics). Typically, optical measurements of objects like plasma columns or flames are integrated along the line of sight.

To obtain the underlying distribution from a measured projection, the inverse Abel transform has to be calculated.

This submission provides a Fourier-based algorithm which extracts the radial (2D) distribution from a one-dimensional projection measurement. The algorithm has been proposed and published by G. Pretzler (Z. Naturforsch. 46a, 639 (1991)). Compared to earlier approaches towards Abel inversion, this algorithm is relatively insensitive to noise and errors in the determination of the object's center (see G. Pretzler et al. , Z. Naturforsch. 47a, 955 (1994)).

The fundamental idea is to fit the whole measured profile to a set of cos-expansion-based integrals. (In the conventional approach, in contrast, the radial distribution is obtained by starting at the edges and incrementally iterating towards the center - making it more prone to errors.)

Carsten Killer (2021). Abel Inversion Algorithm (https://www.mathworks.com/matlabcentral/fileexchange/43639-abel-inversion-algorithm), MATLAB Central File Exchange. Retrieved .

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Necip UnerHyun Jun KimHi, I am almost new in the Matlab and trying to obtain reconstructed distribution using your code.

With a measured profile, I made a new variable as 'h' (1x34 matrix).

I don't understand why this code read your sample data (generate_test_data;) even with the 'h'.

This might be a basic problem, but I would like to ask you about the way to get my result.

Carsten KillerDear Viswa Sunkavalli, sorry for the misunderstanding.

However, I am still not sure I entirely understand your setup. Are both views that you have perpendicular to the axis of symmetry? (i.e. of the object were a candle flame, and one view if from front and one from side). In that case, it should suffice to use only one data set as both are expected to give identical results in an ideal experimental setup with an ideally symmetric object.

Sticking with the cande flame picture, if one view is from front and one is from top, and you want to use both data sets to reconstruct the density field, this simple Abel inversion is not the right choice - this goes more into a direction of a tomographic reconstruction...

Viswa SunkavalliDear Carsten Killer,

Thank you very much for your reply. I apologize for not giving a clear context for my query. Yes I have gone through some of the comments previously and my case is rather similar to @aneps in that it isn't an image I'm applying transform for. I have a mXn array of abel projections of density components along x-axis and another mXn array of abel projections of density components along y-axis each set of which was derived from deflections of back ground image along x and y axis.

Now I have to invert the data to get density field of the air above a jet in space placed between camera and background. I noticed that you have suggested using bilinear interpolation earlier to convert to two independent data sets into one 2D grid. Could you elaborate on that please?

As to applying abel transform on each row because it only takes an array of 1xm - this I have understood.

Carsten KillerIn that case, apply Aben inversion to each row of your image individually, since the reconstruction is independent for each row. That question came up already a few times here, here I am copy+pasting from an earlier reply I made to a similar request:

<quote>

OK, I assume that you have a 1000x1000 image I and the axis of symmetry is vertical in the center of the image, i.e. at x=500. Then, considering the right half of you image (left and right half are independent of each other, but should ideally of course give identical results) you can perform the Abel inversion for line k by:

[f_rec , X] = abel_inversion(I(k,501:end),R,upf);

For the entire image, create a loop through all k and save the result in the k-th row of f

f=zeros(1000,500);

for k=1:1000;

f(k,:)=abel_inversion(I(k,501:end),R,upf);

end;

</quote>

Viswa SunkavalliHello, I have 2D data for Abel transform in my problem i.e. displacement along x and displacement along y directions each a mxn matrix. I wish to reconstruct a 3D field using Abel inversion. Its axisymmetric along y axis. But the code here accepts only 1D data and generates a 2D data . Could you please advice me on how I can work with 2D data using this?

Giselle@carsten: thank you for your explanation, appreciate it.

Carsten Killer@Giselle: The Abel inversion deals with a 2D "object", but it takes a 1D input (e.g. some measured F(y)) and returns a 1D output of the underlying radial profile f(r). Since the Abel inversion assumes cylindrical / polar symmetry, the 2D problem is reduced to a 1D by definition. Of course, the 1D output f(r) can be transformed to a 2D result in the x-y-plane by coordinate transformation.

Giselle@Casten:

By theory, the Abel inversion gives a 2D output of a 1D input. but why in your code the input and the output have the dimension?

About the coordinates, yes, I get it now. it was my misunderstanding.

Carsten Killer@Giselle:

I have to admit that I don't see the point in performing Abel inverison in cartesian coordinates. After all, the Abel inversion assumes a cylindrically symmetric system, and therefore cylindrical / polar coordinates are an obvious choice. Please let me know if I misunderstood your request.

Converting the output (which is a function of radius as you correctly state) to cartesian coordinates can simply be done by a coordinate transformation from polar (radial profile from the Abel inversion + the angle of interest to you) to cartesian (x,y) coordinates

Giselle@Casrten Killer

Hello, I went through all the comments and figured your code works for each row, and the output is a function of radius (r).

Is there any way to convert the output to the cartesian system (X-Y)? Do you have any suggestion about performing Inverse Abel in cartesian system?

Thank you in advance.

albert wwIs this program more suitable for processing circular data?In spherical coordinate system, is the image of another axisymmetric easy to process?

Leigh StangerCarsten KillerIf your simulation setup and synthetic diagnostic results in a problem that can be described as Abel transform ( https://en.wikipedia.org/wiki/Abel_transform ) --> Yes

BHARAT SINGH RAWATI want to get a radial profile from the emmitance plot of a simulated ion beam can I use this inversion for the same?

abdelhafidh moumenDear Bryce Inman,

Thanks a lot for you complete and clear answer. Nevertheless i still have one more question, in my case the reconstructed density has to be done based on two sets of projections (in x and y directions). Do you have any idea how i should implement it?

Thanks

Bryce InmanDear Abdelhafidh,

I have used this code for reconstructing the density distribution from experiments similar to what you described. Dr. Killer's code works very well for this purpose. The Abel inversion is sensitive to the location of the axis of symmetry, so make sure the wake is vertical before processing. I also found it helpful to set R equal to the pixel distance from the axis of symmetry to the edge of the image and then convert to physical units afterward.

Carsten KillerDear Abdelhafidh Moumen,

I am not aware of that particular use case, but I know of various situations which might (?) be similar in terms of data analysis, e.g. 2D images of plasmas, flames, or granular cylindrical objects. Just make sure only input one vector from r=0 to r=r_max at each time, scanning the 2D image line by line

abdelhafidh moumenDear Carsten,

Thanks for sharing this code, I'm trying to get the density distribution for an axisymmetric flow using the background oriented schlieren technique, do you have an experiment or does someone apply your algorithm in a similar configuration

Carsten KillerDear Joe,

if I understand correctly, you obtained spectra at different positions and want to obtain temperature profiles. Without having experience for this particular problem, I would assume the process consists of two steps: first, determine radial profiles of the individual spectral lines, and, second, determine the temperature from the line ratios using some model (or something similar). The Abel transform can only perform the first step, i.e. determine the radial intensity profiles for the different spectral lines.

Without knowing the details of your setup and data structure, I suggest to perform the Abel transform for each spectral position / wavelength individually. If the data is not evenly spaced, it first has to be interpolated on an evenly spaced 1d array which can than be used as input for the Abel inversion.

Joe BransonI am a little confused and maybe you might have some suggestions. I haven't really used matlab before but I think that isnt my main issue. I have data from a plasma column specifically the fulcher bands of Hydrogen and I am trying to pull out a radial gas temperature profile - my function I am looking for is T(r). I have several viewing chords from - lets say 0 - center to N-1 limit of where I could move my fiber + N much futher away from the plasma but not the same travel gap as the rest. The readme suggests the data that go into the function is a 1 x N array. Is this for example the first data point for each of the spectra at each position or would it correspond to something else?

I appreciate your input as I am new to abel inversions for data analysis.

Thanks, Joe

Carsten KillerDear Deepak Singh,

I am not entirely sure how the geometry of your problem looks like, but I am afraid that this code might not work for it. This alrgorithm requires a full profile of data, from the center of the object to its edge, e.g. like a photo of a (symmetric) flame from a candle. I would guess that your data only covers parts of the "object" (which is planet+atmosphere)? In that case, probably a numeric / iterative approach would be more suited.

Deepak SinghDear Carsten,

I am trying to retrieve vertical refractivity profile of planetary atmosphere from radio occultation measurements using Abel's transform. Can you please let me know how to apply your code for my purpose?

Carsten KillerOf course the results will be different, but so will be the units. If you set R=12 , your result be in units of something like emissivity /mm^3. If you set R=1.2 , the result is in units of emissivity / cm^3.

Antonio D'Amato@Carsten Killer Hi Carsten, my doubt is that i can write the my object size as 12 mm or 1.2 cm, obviously, and therefore my radius R would be once 12 mm and another 1.2 cm, giving me the different results that I think should be unique because the size of the object has not changed

Carsten KillerThe algorithm doesn't know how large your object is. So, if you want to get the profile of emissivity per mm^3 and if the input vector for Abel inversion corresponds to an object of size 50mm, the input for R is simply 50.

Antonio D'AmatoHi Carsten,

actually i think i already have the physical quantity, the integrated emission intensity , the value of which is around 2000, even i don't know the unit of measure because it is a fact that my tutor did not give me. Anyway , the shape of the radial distribution is the same, but with radius variation between 0 and 1, the max value of the radial distribution is 1500, while with radius variation between 0 and 50 mm ( the correct range) , the max value of the radial distribution is around 80. Then i don't know what are the correct values.

Carsten KillerHi Antonio,

negative values are a mathematically valid solution of the Abel inversion problem but are of course unphysical. I would guess that this is due to experimental uncertainties such as cylindrical symmetry not being exactly fulfilled, optical thickness of the object (maybe re-absorption of light, refraction due to heat gradients) , or incorrect determination of the center of the object.

Regarding the choice of the units for the radius: this should only influence the magnitude of your resulting profile but not its shape. If you are interested in some absolute physical quantity (e.g. density being inferred from absorption using Beer-Lambert law) then you should set the radius to its correct value (e.g. 50 mm if that is your objects' radius, and you will eventually get a density profile in units of mm^-3)

Antonio D'AmatoHi Carsten,

I have implemented an inverse abel transforme code to recover the radial distribution of a flame emission starting from the projection obtained with an iccd camera. I have referred to your code, but I have problems due to the presence of negative values in this radial distribution. but when I reapply the direct abel transform integral, I recover the initial projection so I do not think it's a code problem. I read a comment that related to this but I did not understand how I can solve the problem. I also wondered if the additions should be made considering normalized rays (between 0 and 1) or real ones (for example between 0 and 50 mm) because the solutions in the two cases are different. thank you

Carsten KillerHi Sung Gyoon Oh,

it is hard to give general advice on a specific problem. The optimum value for upf depends on the kind of noise in your data. I suggest to choose it only as high as you still believe that the small scale structures in the reconstructed profile are real (e.g. if your plasma has no filaments or similar structures one generally expects a relatively smooth emission profile. I also used this code for inversion of plasma emission profiles and typically used upf in the range 20-30).

Regarding the dip at the center: this might be an artifact due to an imperfect estimate for the center position (axis of symmetry) or some slight misalignments in the optical setup (speaking from experience here...)

Sung Gyoon OhHi Carsten, thank you a lot for the codes.

I am trying to reconstruct 2D planar image based on 3D line of sight plasma image which is assumed to have cylinderical symmetry. I tried generating F_rec per each row perpendicular to symmetric axis, and about 150 data points were used for every reconstruction of F_rec. The original h(y) has greatest value at the center and monotonically decay to 0 as it goes to edge, where the profile of h(y) looks like general cos-wave function.However, as I increased the number of upf, which correspond to the number of cos expansions, I found out there seems to be a optimal value around 5~35. Here are the behaviors of F_rec with increasing upf.

At low upf(5~15) the reconstructed profile tend to have profile nearly same as original h(y), where they both look like cos wave. At higher upf(20~30), the profile starts to shows small dip at the center(r=0) with maximum intensity at 0<r_max<R,and at one fixed location. With even higher upf(30~35), the small scale structure start to show up while the overall structure is maintained. For more higher value, noise-looking unsteady peaks are fluctuating on the curves.

I was wondering what is the optimal choices for upf and wanted to know the way I can expect the optimal upf. If you need more information about the explanation above, please send mail to godcapable@gmail.com. Thank you.

Raffaello MarianiThanks,

I will look into that.

Carsten KillerHi Raffaello,

I am not sure how this problem arises. How do you call the function?

plot_results is the 4th input variable and should be either 1 or 0. If you don't provide it as input when you call the function, the variable is generated in line 44 or 53, depending on whether or not you put in data is first input ("h")

Raffaello MarianiHello Carsten,

Thank you for posting the code. I can apply directly my data without any extra coding, but when I run the program I get the following error: "Undefined function or variable 'plot_results'." How can I bypass this problem?

DM Sidben ohayoncooper xiDear Carsten：sorry to bother you again.

my question is to reconstruct 2D chemiluminescence image from a line-of-sight integrated measurement image of a symmetrical flame, hence getting the actual cross profile without accumulating chemiluminescence. I don't know how this code works and where I should change when applying it for my question, could you give me some more specific Instructions to solve my problem. I will be grateful for your reply, my email is xzy1022@163.com, thank you very much.

cooper xi@Carsten Killer:ok,thanks for your reply.

Carsten Killer@cooper xi: Yes, the code can be used for this purpose.

If you are unsure how to use the code, you may scroll through the comments below, where you will find some conversations on how to use the code for these applications. If you are still unsure after that, feel free to contact me with specific questions.

cooper xiDear Carsten,Thanks for sharing your code.i've got a question concerning the treatment of flame structure, can i use this code to reconstruct 2D images from an measured accumulated flame image? looking forward to your help

Brian SeyfarthHello Carsten,

i've got a question concerning the normalization of the resulting data.

I figured out, that there is a need of a factor like "length(rec)/3" (rec is the reconstructed data) to fit the initial and the resulting data, but thats not really exact (still about 0.3% mismatch).

Why is there a odd normalization like this necessarry? Or am i mistaken?

Thaks for your time!

Farzaneh ziaeeThanks for Crasten,

There is still one problem. In the for loop you wrote where is f_rec and X?

Carsten KillerOK, I assume that you have a 1000x1000 image I and the axis of symmetry is vertical in the center of the image, i.e. at x=500. Then, considering the right half of you image (left and right half are independent of each other) you can perform the Abel inversion for line k by:

[f_rec , X] = abel_inversion(I(k,501:end),R,upf);

For the entire image, create a loop through all k and save the result in the k-th row of f

f=zeros(1000,500);

for k=1:1000;

f(k,:)=abel_inversion(I(k,501:end),R,upf);

end;

Farzaneh ziaeeThanks for your reply. I still have a question. By a for loop you mean the whole program or a specific part. I am not sure where should I define this loop. Would you please tell me where to define this loop. I am really appreciated.

Carsten KillerThe algorithm only works for one line at a time, so you will have to call it in a loop 1000 times, each time for one distinct row (or column, depending on the direction of your axis of symmetry) of your dataset.

Farzaneh ziaeeFarzaneh ziaeeHello Carsten,

I need to invert my 2D spectrometer images and to do so I can generate 1000* 1000 matrix. But I do not know how to input this matrix. I really appreciate your help.

A GoswamiWenting HeThanks a lot! Because my data at the edge is fluctuant, so I cannot so I cannot subtract the background by "h2 = h - h(end)". But I'll try to reduce the effect caused by my data at the edge.

It's really nice to discuss with you!

Carsten Killer20 data points is not that much, so the negative result in the center might be an unavoidable result of your limited spatial resolution. Improving the number of data points to 950 by interpolation/fitting does not really add new information, so I am not surprised that this does not change much.

Regarding substracting the background: What I had in my mind does not change the number of data points. If your data is in a 20-element vector "h", just create a new data vector

"h2 = h - h(end)"

which will still contain 20 data points but goes to zero at the edge.

Besides this suggestion, I am afraid that you have to accept the negative results in the center which are probably caused by the spatial resolution of your dataset

Wenting HeThank you very very much Carsten for the patient and professional respond.

I have 20 data points for one Abel inversion. And If I set Nu as 6,then I got negative reconstructed value in the center but if I Nu is 4, then I won't get negative value.

I also tried to subtract the background, then I only have 16 or 13 data points. but it didn't help too much. I still got negative data even I set Nu as 4.Only that I set Nu smaller than 4.

what's more, I also tried to fit the data first and then subtract the background. then I have about 950 data points. however, even in this case, I can obtain positive value only that I set Nu smaller than 6. Therefore, I think Nu have a significant influence on the value in the center of plasma plume but not the number of my data points. Anyway, I don't need very accurate reconstructed value at the edge because the emission at the edge is naturally low.

in my case, do you still have better suggestions?

Carsten KillerHow many data points do you have? In any case, Nu should be considerably smaller than the number of data points.

If the data does not fall to zero at the edge you will get wrong reconstruction results at the edge of your plasma since the basic geometry of Abel inversion requires this boundary condition. Whether this error is restricted to the edge region of your data set or whether it might also affect the plasma center depends, again, on the size of your data set and Nu.

As a test, you could manually substract the background light from your dataset, so that the data at the edge becomes zero. Then you can check whether you still get negative emissivities in the center

Wenting HeMorning Carsten, thank you for your reply. I do get a negative value in the center of plasma column once I set the Nu larger than 5. And if I set Nu as 20, then I will get this warning "Matrix is close to singular or badly scaled. Results may be inaccurate." Maybe I just have a few data. Do you think it is a problem that my data doesn't fall to zero at the edge of plasma column?

Carsten KillerDear Wenting He,

the question for the best choice for Nu is indeed not easy to answer. It depends on your problem, e.g. on the number of data points available. While in general a larger Nu allows for more details to be reconstructed you also emphasize noise artifacts and other uncertainties (e.g. a slightly incorrect determination of the radial center of your plasma)

Of course you are right that a negative plasma emissivity is unphysical. Do you still get negative results for larger Nu (e.g. 10,15,20)? Can you rule out that you have other processes influencing your measurement such as re-absorption of light? (such things might also lead to the appearance of negative emissivities).

Wenting HeHello Carsten, Thanks for sharing your code. It helps a lot. But I still have a question that if I set Nu as 6, I will obtain a negative reconstructed distribution in the center of plasma column. Because my measured profile have a low value in the center of plasma column. I don't think this is correct because the smallest emissivity should be equal or larger than zero. what's the reason for this? PS: if I set Nu as 4 or smaller than 4, the reconstructed distribution won't be negative. But in your explanation, 4 is too low which causes low=pass filtering effect. It looks that the result is highly dependent on the Nu. So how do I know which is the best Nu for my data?

Carsten KillerHi,

"integral" was introduced in Matlab2012. If you use an earlier version of Matlab, just replace "integral" with "quadgk", which should also work fine.

sc schi,

some functions used in your algorism seems cannot be found, such as 'integral' in compute_expansion.m . Did I should download some other toolbox?

Carsten Killer@ot tl: B and L are defined according to equation (8) in the original article by Pretzler, which is in the form A*L=B.

Hence, in my code L is the matrix containing the product of each integral h_n with each other integral h_n. Further, B is defined as the product of the measured data with the integral h_n. On both sides of the equation, we sum up over all positions (index k).

Was this the answer you were hoping for? If not, feel free to ask again.

ot tlHello Carsten, Thanks for sharing your code. I'm trying to go over your code in order to learn how to implement a theoretical mathematical algorithm in MATLAB. However I did not manage to understand the code regarding the solution of the equation system: A*L=B. Can you please explain why did you define the L matrix and B vector the way you did ? ( in particular: what's the meaning of the sums in these definitions ? ) . Thanks a lot !!!

Carsten Killer@F. Salehi: Actually the only reason for using this particular basis function is that it was used in the original article by Pretzler (see description), which inspired this code.

You are right, it should principally also work for simpler basis functions. I have not investigated whether the choice of the basis function has any practical impact on the algorithm.

F.SalehiHi Carsten, Thanks for sharing your scripts here.

I was wondering if there is any specific reason for using (1 - (-1)^n*cos(n*pi*x/R)) as your basis function for expansion instead of simply using cos(n*pi*x/R) ?

This way your basis will be orthogonal.

dj327Hi Carsten, the problem of isqcuivefit not running is solved. A classic 1*N matrix or N*1 matrix problem. Although I made sure the input of h is 1*N matrix as requested, dimension and h and myfun inside lsqcurvefit(myfun,x0,hn,h) don't match...so I just simply transposed h

dj327Thanks for your fast reply, sorry I didn't read through the whole description.

Carsten Killer@dj327: That depends on whether the line of sight is a full secant line (as in most experimental situations) or just a half secant line, which would generally be sufficient for the problem. The code is written for the latter situation (with hindsight maybe not a good choice, but I do not want to change the submitted code for this minor issue for reasons of consistency).

Please note that this issue is already addressed in the last paragraph in the code description above ("UPDATE: ...").

dj327I believe you have missed a factor of 2. I need to divide f_rec by 2 to get the expected result.

Could you please check?

Carsten Killer@aneps: Just process every row (or column, depending on the symmetry axis in your system) separatey. For example, you can call the abel_inversion function 100 times for the 100 rows/colmuns, using a simple loop.

anepsMy data input (H) is a colormap; a matrix of size 100 x 100. When I tried to use this program to perform inverse Abel transform it shows error : "Error using .*

Matrix dimensions must agree" .

I understand the input data set should be 1 X N matrix. How can I use this program in my case where I have an intensity map of mxn matrix (mine is 100x100)? Thank you.

surya NarayanWhenever i mask the data i have does not start from the axis symmetric center but at a position of some pixels off from the center. How to use abel inversion in this case? Please suggest some references.

Carsten KillerCould you please specify what exactly you mean with "masked" ? (In any case, your data has to be smooth enough to comply with the general constraints of the Abel problem.)

surya NarayanI am using the same code for abel inversion of the axis symmetric data. I have a masked region at the center. Abel inversion is giving me a wrong values if i have a mask. What should i do to make the code work? please send me some references if u have any.

surya NarayanCarsten KillerHi Laurel,

if the symmetry axis is in the center of your image, the image has to be "cut in half" for Abel processing, i.e. the left and right half are calculated independently. Please remember to use something like fliplr for the left half, so that the first element of the input vector corresponds to the center of the original image.

In your case, an input vector therefore seems to contain only 64 data points. That is not much - I am not sure how well the algorithm will perform in this case.

If are still not sure whether you use the function correctly , you can send a sample image to killer@physik.uni-greifswald.de and I will take a look.

Cheers, Carsten

LaurelHello,

I'm trying to perform an Abel inversion on a set photographs (128x800) of a flame issuing from a jet (to analyze for emissions). The cylindrical symmetry is oriented along the longer (800) axis. Per previous comments, I've been trying run the Abel function one row at a time (running from 0 to 128). However, the produced results do not appear to be accurate. I also tried cutting the image in half and started my iteration from the centerline of the jet. I am unsure if I am using the function in the correct manner.

email: lpaxton@usc.edu

Thank you

Carsten KillerRecently, the journal (Zeitschrift für Naturforschung) has been digitalized. The paper on Abel inversion can be found on page 639 at

http://www.znaturforsch.com/aa/v46a/c46a.htm

1. Actually, noise is accounted for by using a finite number of cos-expansions. The less expansions you use, the more noise is filtered out (real physical information is of course neglected on the same scale as the noise, so you shouldn't use a too little number of expansion.)

2. You are right, center shift is not included in this code.

nudtThe programm is helpful, but several factors such as noise and center shift are not taken into account.

Could you please share reference 1 to me so that I can understand the theoretical background? my email is jianguotan@hotmail.com

Thank you

Carsten KillerIt is not necessary to figure out a function. Just use a row of your image (with the symmetry axis at the first element of the vector) as the first input of the main function ("h").

(the code works numerically (not analytically), e.g. the polynomial sample function in GENERATE_TEST_DATA is also discretized onto a grid and is not treated as an analytical function)

Dimas AvilaThanks for the speedy reply Carsten! So for each row of my image should I figure out a function that characterizes that row and input that?

Carsten Killer@Dimas Avila: The polynomial function is just an example given in the function GENERATE_TEST_DATA. (the result of this function is shown in the sample image at the top of this page). This function is only called if you do not provide input data.

The data vector that you want to perform the Abel inversion on is the first input variable in the main function. Please perform the Abel inversion for each row/column (depending on whether your symmertry axis is vertical or horizontal) of your image separately.

Dimas AvilaI was trying to perform an Abel inversion on a set of flame photographs I took to look for emission radicals. I was wondering how I can use this program to perform this. I see there is a function which generates a polynomial distribution function and then takes the abel inversion of that function. I just don't know how to do this for an image.

Carsten Killer@Adnan: I don't see any way in which Abel inversion would be related to your problem. You might want to consider some edge detection algorithm (Matlab offers plenty of them) to find the shape of the person in each frame.

Adnan Farooq@Carsten. In my case i have video of a person who is walking in front of camera (we can see the side view of person) and there is nothing at the background. so all the frames consist of each step he took for walking. so i want to apply Abel inversion projection on each frames (similar like making features vector)

Carsten Killer@Adnan: I am not sure what you mean with "finding changes". Of course, in different measurement images, the Abel inversion results of these images will probably differ as well. But please consider that the Abel inversion is only suited for a special situation, i.e. the investigation of symmetrical objects. Of course you can apply the Abel inversion code individually for each row or column, if your data is some kind of line-of-sight integrated measurement of a symmetrical object/system.

If the axis of symmetry is vertical, you have to consider the rows of your images. Please keep in mind that the axis of symmetry is at the start of your input vector (row) , i.e. the first element of the row vector corresponds to the center of your system r=0 and the last element corresponds the the edge, r=R.

Adnan Farooq@ Carsten and Borek, Thanks for your answers. Actually i want to use Abel transform on sequence of images i have to find the changes in that ... so i want to in that case is it possible to apply Abel inversion directly on 2D row wise and column wise..??

Borek@Adnan Farooq

As Carsten wrote, result is a distribution

f(r), where r is the diameter of a symetric circle. It means, the distribution is same for angle phi from 0 to 2pi. To plot f(r,phi) in 2D, the same parametrization can be used. If you need something more sofisticated, see assymetric abel inversion, which can be used for assymetric signals for example for simple plot of irradiation profile of plasma in tokamaks.

Carsten Killer@Adnan Farooq: Could you maybe pose a more specific question? To summarize, this code takes your input F(y) and calculates the inverse Abel transform, resulting in the corresponding f(r). (using the standard notation, e.g. used in http://en.wikipedia.org/wiki/Abel_transform ).

Please note that this code only performs the calculation for one vector, i.e. one row (or column, depending on your systems's geometry) of your image. If you want to transform a complete 2D image, every row (or column...) has to be processed individually.

Adnan FarooqHello Carsten

Thank you for submitting for code. I am studying about Abel Transform and want to use for 2D image.. i want to know that does this code supports?

Carsten Killer@surya Narayan:

1) In your case, only half of the data has to be used, i.e. the symmentry axis is at the beginning of your data vector. From the geometrical point of view, both halves (left and right) are independent. For perfect symmetry, they will of course yield identical results. Therefore, the difference between the left and right half isa good indicator for the quality of symmetry in your system.

2) The radius is important for the scaling of the results. For any arbitrary value of R you will get a qualitatively correct result from the Abel inversion (except for very low values of R << 1 , which should be avoided). But, if you need a quantitatively correct result, you have to use the (outer) radius of your object. (e.g. if you investigated some glowing or light absorbing stuff in a glass cylinder which has a radius of 50 mm , just use R=50 and your result will be scaled to mm units)

surya NarayanI have 2-D unwrapped phase values (axis is at the middle of the data)

1. I am entering the axis symmetric data row wise(vertical symmetry is present) as full row. Is this right or should i give only one half of the data?

2. What is the radius that has to be given as input?

can anyone help me out?

Sina TebianianSina TebianianThanks Carsten, Sorry I wrote by mistake "arrow" instead of array. Anyway my data has a physical range that goes from 0.48 to 1. So I understand that you suggest that I subtract the minimum value of the vector from all its components. Once I run the function, I will add the minimum value to the output data again. I figured the normalization once I went through the mfile. Many thanks for your help.

Sina

Carsten KillerHi Sina,

about the data range: If you use the plot option of my code, both your original data and the calculated radial profile will be plotted normalized to 1 (to make it easer to visually compare the profiles). If you are interested in the correctly scaled data, please use the output (f_rec=abel_inversion(...) ) and plot it manually. (of course, the code uses your original data for the calculations and not the normalized data shown in the figure).

About your data: I am not sure what you mean with an "arrow". However, the boundary value of your data vector (i.e. the last value) should ideally be zero (or something close). This condition is crucial for the algorithm and is imposed by the basic geometry of the situation. If there is some kind of constant background information behind your data, you might want to consider substracting 0.5 in order to create a data vector from 0 to 0.1 (it depends on your specific situation whether this is legitimate).

I hope this helps a bit. Feel free to ask further questions if anything remains unclear.

Carsten

Sina TebianianHi Carsten,

Thanks for your useful code. I tried to run the program with an arrow of my data but the plots produce data that are completely unexpected. The measured profile that must reflect my data seems to be shifted up. My data range goes from 0.51 to 0.6 but then on the profile I see that the measured profile goes from 0.8 to 1. Also the reconstructed profile is completely different from the measured one. I am wondering if I have not understood part of the code. My vector is basically 1x301 that goes from 0.5 to 0.6 therefore the radial profile should not be very different from these values.

I appreciate your help

Sina

Mohammed Ibrahim@Carsten Killer

I am not able to access reference 1, based on which the program is created. It would be great if you can share it with me.

ibrahim@aero.iisc.ernet.in

thanks

Carsten Killer@Mohammed Ibrahim: The "measured distribution" is F(y) and the "reconstructed distribution" is f(r).

(I am sorry for any confusion caused. I thought these denotation for F(y) and f(r) to be practical description for applications in data analysis of physics experiments)

Mohammed Ibrahim@carsten kiler

when i run the abel inversion for a test case i get measured and reconstructed distribution F(y). How do i get the radial distribution f(r)?

ErzbergerCarsten Killer@Akash:

By default, lsqcurvefit is not called unless you set the fifth input parameter to 1. If you try the same dataset without using lsqcurvefit (e.g. setting the fifth input to 0), do you also get an error?

Furthermore, do you also get this error when using the lsqcurvefit routine with the built-in test function (i.e. calling "abel_inversion([],[],10,1,1) ")?

AkashDear Sir

Thanks, Now i am suffering from another kind of problems like

??? Error using ==> lsqcurvefit at 253

Function value and YDATA sizes are

incommensurate.

Error in ==> solve_lsq at 17

A=lsqcurvefit(myfun,x0,hn,h);

Error in ==> abel_inversion at 79

A=solve_lsq(h,hn,x0); % solve for

amplitudes A

please help to understand the things.

Thanks in advance

Carsten KillerHello Akash,

I recently found out that the integral function was introduced in Matlab2012 and is not available in older versions.

However, simply replacing "integral" by "quadgk" should do the job in older Matlab versions.

AkashHello Sir

I am not able to run this program. Their is an error

" Undefined function or method 'integral' for input arguments of type 'function_handle"

I think integral function is missing. Since i am new to matlab so not 100% sure what is going on. Please help me.

Thanks in advance

Carsten Killer@R: I will try it with Octave as soon as possible. With Matlab, your example works for me: If I do this

x=0:0.01:6;

h=2*sqrt(6^2-x.^2);

and then start the function:

abel_inversion(h,6,10)

The result is in my case a more or less constant line at y=2 for 0<x<6 (not minding the numerical insecurities now), which is exactly what one would expect.

From the list in Wolfram Mathworld, you might expect the result to be a constant line at y=1 instead of y=2. This difference of the factor 2 is just the consequence of considering the complete half circle or just one quarter segment of the circle (see e.g. in the sketch in https://en.wikipedia.org/wiki/Abel_transform )

So, your line at $y approx 2$ should be the right result (or at least the approximation to the analytical result y=2 constant). What do you mean with "a few other messy lines"?

RDoes it work with Octave? I tried a couple of analytic function/inversion pairs and it's not even close. For instance: f(x)=2*sqrt(a^2-x^2); Wolfram Mathworld says the inversion sould be PI_a(x), where PI_a(x)=0<x<a? 1:0. With a=6 and number of cos-expansions=10, on a reconstructed distribution graph, I get a line $x \approx 2$ for 0<=x<=6 and a few other messy lines.

Carsten Killer@aneps: OK, I think now I see what your problem is about. The program will not work with scattered data, i.e. a list of x-y-pairs. You will have to bin your data (map it onto a 2D-grid), e.g. with bilinear interpolation.

After doing this, you will have a 2D-matrix which is some kind of a density plot of your measurement (like taking a picture with a camera).

If y is the axis of symmetry, each row of the matrix can be used as input H to obtain the radial distribution at that particular heigth (y-coordinate).

(note that if the axis of symmetry is located in the center of your matrix and not at x=0, you just have to use "half" of the rows. In an ideal measurement, with a perfect symmetry of your observable, the left and right half of the matrix would of course be identical. But in reality this will probably not be the case.)

The radius R is only important if one wants the result to be scaled to the units suiting your experimental setup. If you just want to check wether the algorith works for you, just set R=10 or any other arbitrary value.

The upper frequency defines how many cos-expansions will be used. (or, more precisely, up to which order the expansion is calculated). A low value for UPF will lead to a relatively rough approximation of your data, but it is on the other hend insensitive to (high-frequency) noise. Choosing higher values for UPF will result in a more and more exact calculation, which accounts for ever smaller nuances in your data.

aneps@Carsten Killer: Thank you for the reply. I obtain the data by projecting the electron wave function on a plane detector (electron velocity map imaging). The axis of symmetry is Y axis (the polarization axis of the laser used). This is the 2D projection of a 3D wave function. The recorded data (points on which the electron collapses for each measurement) is a 2D distribution of points. My program records the coordinates (x,y) of each points. So, I have a big data of x,y values. SO, here how should I give the input arguments? I mean, how should I choose H, Radius R(which is unpredictable in this case), upper frequency etc?

Carsten Killer@aneps: How is your data distributed along the x- and y-direction? If y is the axis of symmetry (e.g. the vertical coordinate in an upright standing cylindrical object), then I assume you want to perform the Abel inversion in x-direction.

Just take each row of your image and compute the Abel inversion for each row (i.e. for each y-value, you can of course do this in a loop) seperately, because the algorithm accepts only 1D-vectors as input.

Concerning the polar coordinates: You can put your measured data (which is in cartesian coordinates, I guess) directly into the algorithm.

However, if the axis of symmetry in your dataset is not along the x- or y-axis, you would have the perform some kind of transformation to produce a dataset that has an "easy" symmetry (i.e. in x- or y-direction).

Feel free to ask for more details, if my answer was not helpful enough :)

anepsI have a data points with X and Y coordinates. Can I use this algorithm to find the abel inversion of the data? Should I convert the data into polar coordinates? Could you please advise me how to use this algorithm to get the abel inversion for my data?

JamesI tested this inversion against 3 known analytical abel pairs and found good agreement with this numerical solution. I found that with smooth data with good signal/noise, increasing upf provided a better answer.

JamesI was able to get the code working by replacing lsqcurvefit with a standard non-linear equations solver and simply supplying the residuals. Everything seems to be ok but I still need to through a few theoretical test curves at it. Thanks!

Carsten Killer@James: Thank you for your suggestion, which is quite helpful. I changed that part of the algorithm - now the optimization toolbox is no longer necessary.

JamesWould it be possible to use this code without having the optimization toolbox (lsqcurvefit function)? Does it simply find a scaled coefficient for each of the vectors?