All new activity

Storing strings in waves

mtaylor — Thu, 09 Feb 2012 13:30:16 -0800

I am trying to recall strings from a wave. This seems to work OK, so long as the wave was created within the function itself, however, it gives unexpected results when I access the data from another function.

#pragma rtGlobals=1		// Use modern global access method.
Function test()
	make/T/O testTextWave={"text","goes","in","here"}
	print testTextWave
	print testTextWave[0]
End
 
Function testX()
	wave testTextWave
	print testTextWave
	print testTextWave[0]
End

If you run test(), you get the following output:

•test()
  testTextWave[0]= {"text","goes","in","here"}
  text
•testX()
  testTextWave[0]= {"text","goes","in","here"}
  3.37009e-275

can anyone tell me what I am doing wrong? The testX function can "see" the testTextWave just fine and print it in its entirety, but when asked to produce a single cell, it fails.

Is anyone here using the "NIST SANS data analysis program" written in Igor?

Igor_user — Thu, 09 Feb 2012 17:49:32 -0800

Dear All,

I'm currently using the above mentioned program for analysing some data I acquired from small-angle scattering experiments.

It's a free program downloadable from NIST website and fully compatible with Igor.

So, I'd like to ask if here is any small-angle scattering experts who is familiar with this program.

Best Wishes,

Latex in Igor?

bech — Fri, 03 Feb 2012 13:54:26 -0800

There have been a few attempts to get Igor to use Latex output. Some seem to work but are cumbersome (e.g., loading an image). Direct support in igor would be nice. In the maillist, a recent exchange highlights the need. As one can see from Jim Prouty's response, the equivalent Igor way of including a fraction is a long, difficult to learn / remember string. Moreover, it does not begin to approach Latex's range and control over formatting. For example, with packages, one can distinguish in Latex among \frac, \tfrac, \sfrac, etc. -- each of which does something slightly different. The range of symbols is far larger, etc.

So, having an option to replace Igor's system of control for labels, etc. with Latex syntax would improve the program (and make it easier to learn for those who already know Latex).

________________________________________________________

On Feb 2, 2012, at 5:18 PM, David Nicholls wrote:

> I've been trying to insert a "vertical" fraction character into an annotation on a graph. i.e. I want the equivalent of the LaTex $\frac{1}{2}$
>

From: Jim Prouty
Subject: Re: Vertical fractions in annotations? LaTeX? (Mac)

You can use the escape codes to do this directly:

This is \[1\S1\y-15\L1400\X1\Y1\M\B2\M of the total
________________________________________________________

Column order in a table

patarroyo — Thu, 09 Feb 2012 12:17:30 -0800

Is there a way to reorder columns in a table without creating a new table?

Diagnostic Tools in motofit

mtaylor — Tue, 24 Jan 2012 12:45:23 -0800

I am trying to characterize the fits I am doing with motofit and am interested in the following diagnostics:

1. plot of chi2 error vs. # of trials

Unsure of how to do this, but I think I need to concatenate the chi2 value onto a wave during the evaluation loop and then display this wave. Is there an easier way to do this? Chi2 is displayed in the progress window, so that value is in memory somewhere and should be grabable during execution. My first attempt to do this unfortunately failed.

2. Plot of Coefficient values vs. # of trials

This one I have been able to do somewhat, utilizing /DUMP, which creates the matrix M_gencurvefitpopdump[n][*] where n is the coefficient number. (see attached image) However, there seems to be some problem here, as should I "hold" any variable during the fit, the output matrix is offset in such a way that I get something resembling a plaid shirt on acid (see second attached image). The values are still there, they are just not entered into the matrix in an orderly way. As a work-around, I have chosen to set the range of "Held" parameters to zero, for example varying a parameter between 200 and 200 results in a value of 200 being selected for every trial. I would prefer not to do this, however, as it is slower and clunkier in terms of UI.

The gencurvefit help file indicates the following about /DUMP:

/DUMP At the end of every iteration Gencurvefit will dump the genetic population of the parameters that vary, into a wave called M_gencurvefitpopdump. The wave will be 3D, having dimensions [V_nterms][V_nterms*popsize][]. The number of layers represent the output after each iteration. The first layer is that of the initial guess population and the last layer is that of the population when the fit terminates

However, the matrix is actually 2D and as far as I can tell contains the best (or average?) values of the population after a certain number of generations... which is why my graph was so easy to do in the first place. Did I miss something here? Also, I am able to do thousands of iterations, yet the number of points is much smaller, around 100 or so.

Thanks in advance!

Corrupted PNG file from ImageSave

joerg.kunze — Wed, 08 Feb 2012 15:37:04 -0800

Hi,

a problem description:

Igor 6.2.2.2
Win7
Firefox 10.0
Internet Explorer 9

I create a PNG file e.g. as follows:

•Make/O/U/B/N=(256,256,3) Img = mod(x+y,256)
•ImageSave/O/T="PNGf" Img as "C:Temp:Img1.png"

The resulting PNG file seems to be corrupted. If I try to open it with Firefox or Internet Explorer I get a message "the image cannot be opened, because it contains errors." And that is a problem, because it means, that the resulting graphs cannot be published online.

The resulting PNG file can be correctly viewed with other programs like e.g. GIMP. It is correctly displayed in the Windows file preview. A Quicktime upgrade does not help nor does a Quicktime downgrade. Both used browsers are pretty up to date.

In contrast a PNG file created with the following command can be displayed without problem in Firefox and IE:

•SavePICT/O/T="PNGf"/B=72 as "C:Temp:Img2.png"

So the problem seems to be related to the ImageSave command. Interestingly both browsers are affected, so it could also be connected to the operating system.

Does anyone of you know how to resolve this problem?

Best regards,
Joerg.

P.S.: Despite from this error Igor 6 works pretty fine!

Subtract the background and Converting kinetic energy to binding energy

sghanem — Wed, 08 Feb 2012 08:05:37 -0800

Hi All,

I am a beginner in using Igor and I have some problems:

1- How to subtract the background from a graph?

2- In UPS measurements, How to convert the axis of the kinetic energy to binding energy or how to plot the graph from the beginning with respect to the binding energy?

Thanks,

Sama

Subtract two waves

sghanem — Wed, 08 Feb 2012 09:53:36 -0800

Hi All,

I need to know how to subtract two waves?

Thanks,

Sama

Newbie: templates

jlawrence — Mon, 19 Sep 2011 20:21:05 -0700

No matter how many times I read the manual and forums, I still can't figure out this well for opening a template and apply the setting to the graph.
I hope some of you are/were OriginLab/ Kaleidagraph users.
The way it works for me is like this: I made a graph, modify it here and there and save it as template. That way, I can create template for each graph of IR, UV=VIS, NMR, I-V, etc etc). Open new data, plot, and then open plot=templatd-data.

However the present settings are confusing to me. How should I proceed ?

mie scattering code

gmwaniki — Thu, 15 Dec 2011 14:09:18 -0800

I am currently working on a project that requires mie scattering calculation. Most of the code available is in IDL, does anyone have an igor code to do this? I will highly appreciate a timely response.
Thank you

Using GlobalFit to evaluate differences between two different fitting functions

arzensekd — Sun, 29 Jan 2012 15:53:23 -0800

Hi,

I have two different fitting functions which they both have the same first fitting coefficient, but different second one. I want to use them as fitting functions on same data sets. So, for each data set I have to use both functions. Here are my questions regarding this case:
1) What are the benefits of using GlobalFit in contrast to regular separate curve fitting with FuncFit, or is just faster method?
2) Is in this case useful to use GlobalFit like in case of two different functions for two different data sets?
3) What do you recommend to use for comparison of two different fitting functions only in one parameter on the same data set?

Thank you for all information and advices.

Best,
Dejan

GetFileFolderInfo usage and flags

tech- — Mon, 06 Feb 2012 08:35:44 -0800

Hi, I'm using Igor Pro 4 ans would like to use GetFileFolderInfo to check whether a file exists on a local disk. However I can't find the command in the Igor help or online. Is it only available in later Igor versions? Are there alternatives I can use to check whether a file exists with Igor 4?

If it is possible to use GetFileFolderInfo, could you please post the correct usage explanation as I am not sure which flags to set.

Image Plot from matrix data

MarkusG — Sat, 24 Sep 2011 02:25:53 -0700

Hello!

I would like to start by explaining how far I got on my own before I ran into the problems I am addressing here. Maybe there is some alternative along the way that will make the actual problem not appear in the first place.

I am starting with data that is in what I call "gnuplot format":

x1 y1 z11
x1 y2 z12
x1 y3 z13

x2 y1 z21
x2 y2 z22
...

I didn't find out whether this can be processed directly by Igor so I extracted three files from it with python which are (x1,x2,...), (y1,y2,...), and the matrix with the z-values. These I load into Igor which allows me to plot the matrix as an image with the x- and y-wave (after adding one additional point) as the corresponding axes.

The first problem is that I think the z-values in the matrix lose the knowledge about the x- and y-values they belong to. So it is up to me to set the right order for the axes. In this case I know how the image is supposed to look like but once I don't, how can I be sure which order of x- and y-values is correct?

The second and more important thing to me right now is, that I have two such matrices, one running from y = 0 to 3 Tesla the other one from y = 0 to -3 Tesla. I would like to plot them in the same image plot. Is there a way to correctly join the two matrices in Igor? For that I would have to mirror the second matrix so that it runs from -3 to 0 Tesla. Only changing the order in the y-wave doesn't help because as I said above, the z-values are not connected to their "real" coordinates any more.

Ok, I hope I followed all the forum rules correctly and there aren't too many typos.

Thanks for any help,

Markus

box plot of average diurnal variations

lcrilley — Wed, 01 Feb 2012 16:59:41 -0800

Hi,
I am new to IGOR and my data is 5 min concentration of chemical species over a couple of weeks like so

1/09/2011 18:05 0.311107
1/09/2011 18:10 0.277637
1/09/2011 18:15 0.282964
1/09/2011 18:20 0.232187

I would like to do a box plot by the hour ie showing the mean, median etc for each hour of the day over the length of my data. I am aware of the decimation function which will average the data by the hour for me but the problem is where I have data missing, the function will give a blank cell for that hour even though there are other points during that hour period. Is there a way to get it calculate the average when there is missing data?
I would also appreciate any help with sorting the data by the time of day.
Any help would be greatly appreciated as I am struggling with this.

Understanding Hough Transform Output

hegedus — Mon, 06 Feb 2012 15:09:53 -0800

I am starting to play with the Hough transform to analyze some images.

The data is the result of microscopic inspection of sample and the x-y locations of a defect. The question we are trying answer and quantify is are the defects the result of a larger effect.

I create a binary image with the dots representing the XY locations. I do a Hough transform and then I used particle analysis to identify the hot spots.

As I understand the output the Row value should be the angle and the column should be the radial distance and the reference point should be the center of the image.
"The result is saved to a 2D wave M_Hough in which the rows are the angle domain and the columns are the radial domain."
The transform picks up four lines and that corresponds to the image. and if I look at the data from particle analysis. First it seems as it is switched. If we assume that the original image was scaled to 100 by 100 and if the reference point is 50,50 (center of the image) then for points that are 0 or ~180 (173) the greatest possible distance is 50, but they are listed at an assumed ~70.
X Y
70 0
44 88
55 153
71 173

I have obviously done something wrong, so how do I get back on track?

MatrixOp precision?

BMangum — Sat, 04 Feb 2012 08:38:54 -0800

I have found a problem that when using MatrixOp I sometimes get bad values.
When I substitute the equivalent Make command, all is right with the world.
Is this due to the precision of MatrixOp?
Is there some other problem with my code?

(Using 32 bit Igor 6.22A with 64bit Win7)

here is the example code where I find the problem
The MatrixOp command gives some badvals while the commented out Make command generates none:

 
Function test()
 
Make/D/O/N = 100E6 noise = enoise(0.5)+ 0.5
Extract/INDX/O noise, test0, noise < 0.01
Sort test0, test0 //Make sure the wave is monotonically increasing (should be anyway, but just to make sure I am not dumb)
 
Make/D/O/N = (numpnts(test0)) test1 = expnoise(100)
Print wavemax(test1) // Make sure that the max val does not exceed 2000
 
MatrixOp/O results = test0*2000 + test1
//Make/D/O/N=(numpnts(test0)) results = test0*2000 + test1
 
Differentiate/Meth=2/EP=1 results/D=resultsdiff
Extract/INDX resultsdiff, badvals, resultsdiff < 0
 
End

Acquire data from serial port (RS232) and USB simultaneously?

crazytooguy — Mon, 06 Feb 2012 10:55:23 -0800

Hello!

I need to monitor and record the data from an RS232 temperature readout (Lakeshore 218), and from a USB DAQ reading control voltages at the same time. I want the data to appear in a single Igor session. I currently read the Lakeshore on up to eight channels, although I only need six of those. Can I add a plot of voltage vs time from a USB DAQ to this experiment easily, or am I limited to one serial port at a time? Thanks.

multidimensional maximum

hopper — Mon, 30 Jan 2012 13:46:10 -0800

Hey,

I'm new to Igor and trying to create a function to mass process a series of images. Essentially what I need to do is find the maximum column and row number where z equals 0. I've used the image processing features in Igor to generate a gray scale image and used edge detection so that the image only has two z values, 0 and 255.

Any help is greatly appreciated.

Hopper

load data into Igor changes my data file's time of last modification?

JeX — Fri, 03 Feb 2012 21:31:41 -0800

I'm using Igor on both winXP and win7. Sometimes I transfer projects from winXP to win7. My projects includes lots of data files. I would like to import the data into .pxp file w/o changing anything on the source files. However, the loading process will change the file's Date Modified. Could anyone tell me how to avoid it?

I use loadwave like this: LoadWave/Q/D/O/P=filePath fileName

Weird thing is that it was not doing that at the beginning. I don't quite remember when it started doing this.

Igor crashes on Windows 7

paolovil — Thu, 02 Feb 2012 14:45:23 -0800

Good evening,
I'm experiencing problems with Igor 6.12A running on Windows 7.
After running an update of windows, virus scan etc. Igor started to crash: it got frozen, I cannot execute any operation except that closing using task manager?
did this ever happen to anyone? does someone know how to fix this?

thanks

Issue with ErrorBars in Function

mvwilcox — Fri, 03 Feb 2012 12:31:29 -0800

Hi there,

I'm working on displaying error bars on a graph and can't seem to get around this error message: "When executing ErrorBars, the following problem occured: trace is not on graph".

Here is the bit of the function I'm working with:

		//get info on the source graph
		String yAxisName= StringByKey("YAXIS", TraceInfo(theGraphName, theTraceName,0))	
		String axType= StringByKey("AXTYPE", AxisInfo(theGraphName,yAxisName))			
		String EbarStr = "SEM_" + newTraceName[5,strlen(newTraceName)]
		//display the first trace or append the traces
			strswitch(axType)
				case "right":
					if (isXY)
						AppendToGraph /R=$YAxisName theNewTrace vs newXWave
						ErrorBars theNewTrace Y,wave=($EbarStr,$EbarStr) 
						Edit newXWave
					else
						AppendToGraph /R=$YAxisName theNewTrace
						ErrorBars theNewTrace Y,wave=($EbarStr,$EbarStr) 
					endif
					execute /q StringByKey("SETAXISCMD", AxisInfo(theGraphName,yAxisName))	 
				break
				default:
					if (isXY)
						AppendToGraph theNewTrace  vs newXWave
						ErrorBars theNewTrace Y,wave=($EbarStr,$EbarStr) 
						Edit newXWave
					else
						AppendToGraph theNewTrace 
						ErrorBars theNewTrace Y,wave=($EbarStr,$EbarStr) 
					endif
					execute /q StringByKey("SETAXISCMD", AxisInfo(theGraphName,yAxisName))	 
			endswitch

I'd love to learn why this is happening. The error bar waves certainly exist in the root. Can I use the $ operator to reference these waves? Thank you for any help you can provide.

Cheers,
MVW

Custom peak function in MPF2 - what happened to the fit wave?

josh_ld — Wed, 25 Jan 2012 09:33:15 -0800

I am using Multi Peak Fitting 2 to treat some x-ray photoemission spectroscopy (XPS) data. The model lineshape for the peaks is the so-called Doniac-Sunjic function, an asymmetric Lorenzian-like peak given analytically by

DS(a, G, A, x0) = A*( cos( Pi*a/2 + (1-a)*arctan((x-x0)/G) ) / (G^2 + (x-x0)^2)^(1/2-a/2)
Here A is the amplitude, G is the width, x0 is the centroid, and a is the asymmetry parameter. With a=0 the function simplifies to a Lorentzian, and with a between 0 and 1 it is asymmetric towards lower values of x. Typical fit values of a should be 0.1-0.3.

I believe I have successfully programmed this as an MPF2 fit function, and I can get the peaks to show up in the subcomponent axis. The fit appears to complete correctly, giving me reasonable-looking peaks. However, the fitted curve is not present on the graph - the original data is there, and the residuals look as if no fit is present (direct copy of the data, so it's subtracting zero from the data), see the attached image.

If I switch the peak type to Gaussian, it works correctly. The fit function reappears, and the residuals are calculated properly as well...

Have I messed up the peak definition? Why is it drawing the individual peaks, but not the fit function? Is it the arctangent function screwing me up?

How to create a blinking image marker?

s.r.chinn — Thu, 02 Feb 2012 07:38:22 -0800

I have a 2-D image graph, and want to put a blinking marker on the display. This marker should be relatively small, and blink as rapidly as possible (up to 4 Hz) for ease of perception. My approach has been to use a drawing object, and get it to update as rapidly as possible. I have tried to adapt one method described in the IP manual, but have not succeeded in my goals. I am hoping someone can show me where I am going wrong, or suggest an alternate approach. The code shown clears the old marker, shows a new marker, but does not blink further, even though the loop has five iterations. The only marker attribute that needs to change is from fillfgc=(....) with specified colors, to fillpat=0 (transparent). An alternative would be to remove and redraw the marker, but I had no better luck with that.

function drawdot(x,y, contrast)
	variable x, y, contrast
	variable ticks0,  j
	variable color = 65535/2 + contrast*65535/2    //	sets the blinker contrast in the autoscaled image
	SetDrawLayer /W=Graph2/K  UserFront           //	clear old draw objects
	SetDrawLayer /W=Graph2 UserFront
 
	for(j=0;j<5;j+=1)	//	blink loop
	     SetDrawEnv gstart, gname = greydot
	     SetDrawEnv xcoord= bottom,ycoord= left,fillfgc= (color,color,color),linethick= 0.00
	     DrawOval /W=Graph2  x, y, x-0.02, y-0.02	//  a variable greyscale fill pattern
	     SetDrawEnv gstop
	     DoUpdate/W=Graph2
 
	     ticks0 = ticks
	     do
	     while( (ticks-ticks0)<60 )	//	delay one second, for example
 
	     DrawAction getgroup=greydot, delete, begininsert
	     SetDrawEnv gstart, gname = greydot
	     SetDrawEnv xcoord= bottom,ycoord= left,fillpat=0 ,linethick= 0.00 // no fill
	     DrawOval /W=Graph2  x, y, x-0.02, y-0.02	  // effectively invisible
	     SetDrawEnv gstop
	     DrawAction endinsert
	     DoUpdate/W=Graph2
 
	     ticks0 = ticks
	     do
	     while( (ticks-ticks0)<60 )
	endfor
end

Igor on Linux ???

hrodstein — Wed, 17 Feb 2010 00:34:08 -0800

We are often asked if we might port Igor to Linux. The answer is that it is a possibility for the future but not the near future.

Some Igor users have reported success running Igor on Linux under Wine or under Crossover Office which, as I understand it, is a commercialized version of Wine.

If you have comments about Igor on Linux or want to encourage (or discourage) us from porting to Linux in the future, feel free to add your comments here.

V_r2

gmwaniki — Tue, 31 Jan 2012 16:40:01 -0800

When fitting a line into a data set the V_r2 represent the correlation coefficient right?, If this is true when you force the best fit line to pass through the origin (0,0) the V_r2 seem to improve, and I don’t think that is right.... What is the best to get a true V_r2 value if the line is forced through 0,0