Category Archives: adventures in code

Adventures in Code IV: correcting filenames

A large amount of time doing data analysis is the process of cleaning, importing, reorganising and generally not actually analysing data but getting it ready to analyse. I’ve been trying to get over the idea to non-coders in the group that strict naming conventions (for example) are important and very helpful to the poor person who has to deal with the data.


Things have improved a lot and dtatsets that used to take a few hours to clean up are now pretty much straightforward. A recent example is shown here. Almost 200 subconditions are plotted out and there is only one missing graph. I suspect the blood sugar levels were getting low in the person generating the data… the cause was a hyphen in the filename and not an underscore.

These data are read into Igor from CSVs outputted from Imaris. Here comes the problem: the folder and all files within it have the incorrect name.

There are 35 files in each folder and clearly this needs a computer to fix, even if it were just one foldersworth at fault. The quickest way is to use the terminal and there are lots of ways to do it.

Now, as I said the problem is that the foldername and filenames both need correcting. Most terminal commands you can quickly find online actually fail because they try to rename the file and folder at the same time, and since the folder with the new name doesn’t exist… you get an error.

The solution is to rename the folders first and then the files.

find . -type d -maxdepth 2 -name "oldstring*" | while read FNAME; do mv "$FNAME" "${FNAME//oldstring/newstring}"; done
find . -type f -maxdepth 3 -name "oldstring*.csv" | while read FNAME; do mv "$FNAME" "${FNAME//oldstring/newstring}"; done

A simple tip, but effective and useful. HT this gist

Part of a series on computers and coding

Adventures in Code III: the quantixed ImageJ Update site

We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others.

I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the quantixed ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.

The code is maintained in this GitHub repo, which has a walkthrough for figure-making in the README. So, if you’d like to make figures the quantixed way, adding ROIs and zooms, then feel free to give this code a try. Please raise any issues there or get in touch some other way.

Disclaimer: this code is under development. I offer no guarantees to its usefulness. I am not responsible for data loss or injury that may result from its use!

Update @ 10:35 2016-12-20 I should point out that other projects already exist to make figures (MagicMontage, FigureJScientiFig). These projects are fine but they didn’t do what I wanted, so I made my own.

Tips from the blog X: multi-line commenting in Igor

This is part-tip, part-adventures in code. I found out recently that it is possible to comment out multiple lines of code in Igor and thought I’d put this tip up here.

Multi-line commenting in programming is useful two reasons:

  1. writing comments (instructions, guidance) that last more than one line
  2. the ability to temporarily remove a block of code while testing

In each computer language there is the ability to comment out at least one line of code.

In Igor this is “//”, which comments out the whole line, but no more.


This is the same as in ImageJ macro language.


Now, to comment out whole sections in FIJI/ImageJ is easy. Inserting “/*” where you want the comment to start, and then “*/” where it ends, multiple lines later.


I didn’t think this syntax was available in Igor, and it isn’t really. I was manually adding “//” for each line I wanted to remove, which was annoying. It turns out that you can use Edit > Commentize to add “//” to the start of all selected lines. The keyboard shortcut in IP7 is Cmd-/. You can reverse the process with Edit > Decommentize or Cmd-\.


There is actually another way. Igor can conditionally compile code. This is useful if for example you write for Igor 7 and Igor 6. You can get compilation of IP7 commands only if the user is running IP7 for example. This same logic can be used to comment out code as follows.


The condition if 0 is never satisfied, so the code does not compile. The equivalent statement for IP7-specific compilation, is “#if igorversion()>=7”.

So there you have it, two ways to comment out code in Igor. These tips were from IgorExchange.

If you want to read more about commenting in different languages and the origins of comments, read here.

This post is part of a series of tips.

The International Language of Screaming

A couple of recent projects have meant that I had to get to grips more seriously with R and with MATLAB. Regular readers will know that I am a die-hard IgorPro user. Trying to tackle a new IDE is a frustrating experience, as anyone who has tried to speak a foreign language will know. The speed with which you can do stuff (or get your point across) is very slow. Not only that, but… if you could just revert to your mother tongue it would be so much easier…

What I needed was something like a Babel Fish. As I’m sure you’ll know, this fish is the creation of Douglas Adams. It allows instant translation of any language. The only downside is that you have to insert the fish into your ear.

The closest thing to the Babel Fish in computing is the cheat sheet. These sheets are typically a huge list of basic commands that you’ll need as you get going. I found a nice page which had cheat sheets which allowed easy interchange between R, MATLAB and python. There was no Igor version. Luckily, a user on IgorExchange had taken the R and MATLAB page and added some Igor commands. This was good, but it was a bit rough and incomplete. I took this version, formatted it for GitHub flavored markdown, and made some edits.

The repo is here. I hope it’s useful for others. I learned a lot putting it together. If you are an experienced user of R, MATLAB or IGOR (or better still can speak one or more of these languages), please fork and make edits or suggest changes via GitHub issues, or by leaving a comment on this page if you are not into GitHub. Thanks!


Here is a little snapshot to whet your appetite. Bon appetit!



The post title is taken from “The International Language of Screaming” by Super Furry Animals from their Radiator LP. Released as a single, the flip-side had a version called NoK which featured the backing tracking to the single. Gruff sings the welsh alphabet with no letter K.

Adventures in code II

I needed to generate a uniform random distribution of points inside a circle and, later, a sphere. This is part of a bigger project, but the code to do this is kind of interesting. There were no solutions available for IgorPro, but stackexchange had plenty of examples in python and mathematica. There are many ways to do this. The most popular seems to be to generate a uniform random set of points in a square or cube and then discard those that are greater than the radius away from the origin. I didn’t like this idea, because I needed to extend it to spheroids eventually, and as I saw it the computation time saved was minimal.

Here is the version for points in a circle (radius = 1, centred on the origin).


This gives a nice set of points, 1000 shown here.


And here is the version inside a sphere. This code has variable radius for the sphere.


The three waves (xw,yw,zw) can be concatenated and displayed in a Gizmo. The code just plots out the three views.


My code uses var + enoise(var) to get a random variable from 0,var. This is because enoise goes from -var to +var. There is an interesting discussion about whether this is a truly flat PDF here.

This is part of a bigger project where I’ve had invaluable help from Tom Honnor from Statistics.

This post is part of a series on esoterica in computer programming.

Adventures in code

An occasional series in esoteric programming issues.

As part of a larger analysis project I needed to implement a short program to determine the closest distance of two line segments in 3D space. This will be used to sort out which segments to compare… like I say, part of a bigger project. The best method to do this is to find the closest distance one segment is to the other when the other one is represented as an infinite line. You can then check if that point is beyond the segment if it is you use the limits of the segment to calculate the distance. There’s a discussion on stackoverflow here. The solutions point to one in C++ and one in MATLAB. The C++ version is easiest to port to Igor due to the similarity of languages, but the explanation of the MATLAB code was more approachable. So I ported that to Igor to figure out how it works.

The MATLAB version is:

>> P = [-0.43256      -1.6656      0.12533]
P =
   -0.4326   -1.6656    0.1253
>> Q = [0.28768      -1.1465       1.1909]
Q =
    0.2877   -1.1465    1.1909
>> R = [1.1892    -0.037633      0.32729]
R =
    1.1892   -0.0376    0.3273
>> S = [0.17464     -0.18671      0.72579]
S =
    0.1746   -0.1867    0.7258
>> N = null(P-Q)
N =
   -0.3743   -0.7683
    0.9078   -0.1893
   -0.1893    0.6115
>> r = (R-P)*N
r =
    0.8327   -1.4306
>> s = (S-P)*N
s =
    1.0016   -0.3792
>> n = (s - r)*[0 -1;1 0];
>> n = n/norm(n);
>> n
n =
    0.9873   -0.1587
>> d = dot(n,r)
d =
>> d = dot(n,s)
d =
>> v = dot(s-r,d*n-r)/dot(s-r,s-r)
v =
>> u = (Q-P)'\((S - (S*N)*N') - P)'
u =
>> P + u*(Q-P)
ans =
    0.2582   -1.1678    1.1473
>> norm(P + u*(Q-P) - S)
ans =

and in IgorPro:

Function MakeVectors()
	Make/O/D/N=(1,3) matP={{-0.43256},{-1.6656},{0.12533}}
	Make/O/D/N=(1,3) matQ={{0.28768},{-1.1465},{1.1909}}
	Make/O/D/N=(1,3) matR={{1.1892},{-0.037633},{0.32729}}
	Make/O/D/N=(1,3) matS={{0.17464},{-0.18671},{0.72579}}

Function DoCalcs()
	WAVE matP,matQ,matR,matS
	MatrixOp/O tempMat = matP - matQ
	MatrixSVD tempMat
	Make/O/D/N=(3,2) matN
	Wave M_VT
	matN = M_VT[p][q+1]
	MatrixOp/O tempMat2 = (matR - matP)
	MatrixMultiply tempMat2, matN
	Wave M_product
	Duplicate/O M_product, mat_r
	MatrixOp/O tempMat2 = (matS - matP)
	MatrixMultiply tempMat2, matN
	Duplicate/O M_product, mat_s
	Make/O/D/N=(2,2) MatUnit
	matUnit = {{0,1},{-1,0}}
	MatrixOp/O tempMat2 = (mat_s - mat_r)
	MatrixMultiply tempMat2,MatUnit
	Duplicate/O M_Product, Mat_n
	Variable nn
	nn = norm(mat_n)
	MatrixOP/O new_n = mat_n / nn
	//new_n is now a vector with unit length
	Variable dd
	dd = MatrixDot(new_n,mat_r)
	//print dd
	//dd = MatrixDot(new_n,mat_s)
	//print dd
	dd = abs(dd)
	// now find v
	// v = dot(s-r,d*n-r)/dot(s-r,s-r)
	variable vv
	MatrixOp/O mat_s_r = mat_s - mat_r
	MatrixOp/O tempmat2 = dd * mat_n - mat_r
	vv = MatrixDot(mat_s_r,tempmat2) / MatrixDot(mat_s_r,mat_s_r)
	//print vv
	//because vv > 1 then closest post is s (because rs(1) = s) and therefore closest point on RS to infinite line PQ is S
	//what about the point on PQ is this also outside the segment?
	// u = (Q-P)'\((S - (S*N)*N') - P)'
	variable uu
	MatrixOp/O matQ_P = matQ - matP
	MatrixTranspose matQ_P
	//MatrixOP/O tempMat2 = ((matS - (matS * matN) * MatrixTranspose(MatN)) - MatrixTranspose(matP))
	Duplicate/O MatN, matNprime
	MatrixTranspose matNprime
	MatrixMultiply matS, matN
	Duplicate/O M_Product, matSN
	MatrixMultiply M_Product, matNprime
	MatrixOP/O tempMat2 = ((matS - M_product) - matP)
	MatrixTranspose tempMat2
	MatrixLLS matQ_P tempMat2
	Wave M_B
	uu = M_B[0]
	// find point on PQ that is closest to RS
	// P + u*(Q-P)
	MatrixOp/O matQ_P = matQ - matP
	MatrixOp/O matPoint = MatP + (uu * MatQ_P)
	MatrixOP/O distpoint = matPoint - matS
	Variable dist
	dist = norm(distpoint)
	Print dist

The sticking points were finding the Igor equivalents of

  • null()
  • norm()
  • dot()
  • \ otherwise known as mldivide

Which are:

  • MatrixSVD (answer is in the final two columns of wave M_VT)
  • norm()
  • MatrixDot()
  • MatrixLLS

MatrixLLS wouldn’t accept a mix of single-precision and double-precision waves, so this needed to be factored into the code.

As you can see, the Igor code is much longer. Overall, I think MATLAB handles Matrix Math better than Igor. It is certainly easier to write. I suspect that there are a series of Igor operations that can do what I am trying to do here, but this was an exercise in direct porting.

More work is needed to condense this down and also deal with every possible case. Then it needs to be incorporated into the bigger program. SIMPLE! Anyway, hope this helps somebody.

The post title is taken from the band Adventures In Stereo.