matrix math: finding random solution

ChrLie — Wed, 19 Jun 2013 05:30:35 -0700

I have a NxM matrix AA and a wave bb with M rows. Now I'd like to find random elements in a wave cc with N rows such that, if I execute:

function foo (AA, cc)
	wave AA, cc
 
	Duplicate/FREE/O AA, frac
	frac = AA[p][q] *cc[p] 
	MatrixOP/O bb_calc = (SumCols(frac))^t	
end

bb_calc and bb are identical. A constraint is that all elements in cc must be > 0.

E.g., if AA is:
aa[0][0]= {1,2,2,0,0,1,0,0,0,1}
aa[0][1]= {0,0,0,1,2,1,1,0,0,0}
aa[0][2]= {0,0,1,0,0,0,1,1,2,1}

and bb:
bb[0]= {2,1,1}

a possible solution would be:

cc[0]= {0.5,0.15,0.5,0.5,0.15,0.1,0.1,0.05,0.125,0.1}

I'd be grateful about ideas and suggestions!

Category plot. Stroke color for error bars

sjr51 — Mon, 21 Jan 2013 23:40:46 -0800

When I make a category plot I colour the bars differently according to condition etc., but I would like to have the outline (stroke) of the bar AND the error bar to be black. As I see it there is no possibility to do this. The error bar stays the colour of the bar. My current workaround is to plot a second category plot on top of the original with black but empty bars. Is there a simpler way?

Thanks for any help.

graph

simcacl — Wed, 19 Jun 2013 12:11:41 -0700

Hi all,

Do you know how to make a graph similar to the picture?

Thanks

Simone

pre-triggered scanning

RJS — Fri, 31 May 2013 13:56:01 -0700

Hi All,

I am trying to find a way to (pre-) trigger scanning of diff. channel AI 0 (68 and 67 on my board) using the analogue signal coming into this channel itself. To be precise, I am trying to periodically record 10-30 seconds of EMG (electromyography) signals only when they reach a certain threshold voltage, over an undetermined amount of time (and save them into different waves, but that's not important right now).

Sofar I have been trying to use the Scan Control panel (NIDAQmx) settings but without much success, as its not letting me set the input channel AI 0 as the trigger channel.

Other than splitting my data cable and feeding one half into the AI 0/AI GND and the other into another analogue trigger channel, is there any way this can be done?

Cheers,

Ruud

Loading spectroscopic data into igor from general text

McIlhenny — Sun, 29 Apr 2012 05:20:07 -0700

Hello all,

I've to load a ascii file with x and y waves into igor. A typical file looks like:

Area1

SUR
1
1399.0000,7242.7033
1398.2000,8228.6017
1397.4000,7379.5712
1396.6000,7491.0938
1395.8000,7897.0668
1395.0000,7162.2372
1394.2000,7876.3272
1393.4000,7402.1067
1392.6000,7568.9746

Area1

N1s
1
408.0000,101.1882
407.9500,101.3558
407.9000,96.7365
407.8500,96.9283
407.8000,94.1598
407.7500,94.8345
407.7000,95.6612
407.6500,95.3786
407.6000,94.0064
407.5500,95.0241
407.5000,98.0092
407.4500,99.6761

There are several of such datablocks with different numbers of rows in my ascii file. Each datablock begins with "Area1" followed by a free line and some information from the spectra "SUR, N1s ....". The real data starts after the "1".
Now I want igor to load the data and give the waves special names. Let's say the ascii file is called "Spec1.txt". Then all the xwaves should have the prefix "Spec1_EB_" and all the y waves should be named like "Spec1_Int_". After the last underscore I want to have some data from the header in the wavename. In my example I want the waves to be named "Spec1_EB_SUR", "Spec1_Int_SUR" for the first block and "Spec1_EB_N1s", "Spec1_Int_N1s" for the second block.
My igor skills so far are not good enough to get this job done. I don't want you to give me the total code for this. I'm satisfied with some hints so I can learn how to do this.

Thanks in advance.

how to display smoothing spline integration equation

temasi — Tue, 18 Jun 2013 01:17:35 -0700

Hi all,
Is it possible to display the equation of a wave after fitting using smoothing spline interpolation?
I need the equation to calculate the area between two of this waves/curves.

Any comment will be appreciated.

Thank you

Igor position at Oxford instruments, Asylum Research

Bemis — Mon, 17 Jun 2013 16:05:48 -0700

Oxford Instruments

Location: Santa Barbara, CA
Salary: $TBD plus benefits

GUI Programmer

Asylum Research, an Oxford Instruments company and the technology leader in scanning probe/atomic probe microscopy, is seeking an experienced GUI Programmer to design and develop software interfaces in a flexible, fast-paced collaborative environment for this growing business. This business is part of a successful and rapidly expanding global company, Oxford Instruments plc, a leading provider of high technology tools and systems for industry and research. Located in Santa Barbara, California, Asylum is dedicated to providing innovative instrumentation for nanoscience and nanotechnology customers worldwide.

The Role
We are currently seeking a GUI Programmer with a passion for contributing to our knowledge base and the efforts of our software team. As a key contributor, you will design interfaces which reflect the input of our staff scientists using Igor Pro.
In addition, you will be responsible for providing technical support for
• Users and staff scientists for software use
• Rapid lightweight interfaces
• Responsive bug fixes for existing features

The successful candidate will have
• Minimum 4 year science or technical degree, advanced degree preferred
• Experience with large scale (30+ users), long term software projects, preferably in an AFM (atomic force microscopy) or related scientific environment.
• Experience in advanced GUI programming (Igor, Matlab, LabView, Origin) and Usability design.
• Demonstrated ability to work as part of a small team, handling projects from inception through development and delivery.
• Ability to function well in a fast paced and user focused environment
• Excellent oral, written and presentation skills

We provide a competitive salary and excellent benefits program including medical, dental, vision and 401K programs. To apply, visit the Career section on our website at www.oxinst.com or send resume to Marianne.gruber@oxinst.com along with cover letter and salary expectations. For further information, watch our company informational video at www.youtube.com/oxinst or follow us at www.twitter.com/oxinst www.facebook.com/oxinst.

Shapiro Wilk test for Normality

jelizardi — Sun, 16 Jun 2013 11:45:42 -0700

Does anyone know how to do or create a function for the Shapiro Wilk test in Igor?

Fitting curves erratic behavior?

calmodulin — Sat, 15 Jun 2013 14:33:41 -0700

I'm new to Igor and, when I was trying to do a non-linear curve fitting, I bumped into this strange situation.

Namely, as the attached image (weirdfit.png) shows, the fitted curve became a straight line for x<5. Despite the apparently incorrect graphics, the parameters I got from the non-linear fit are correct--I used Prism Graphpad to analyze the same data set and the resulting parameters are the same. Also, when I key in the parameters' fitted value in Igor's dialog window and hit 'graph it', I actually got a beautifully fitted curve, with no weird straight lines (shown in correctfit.png)!

Thank you in advance for all suggestions and input!

Strange fitting curve

calmodulin — Sat, 15 Jun 2013 14:33:05 -0700

Correlation (R2) between two plots

tsaha — Fri, 14 Jun 2013 08:20:55 -0700

I have two sets of data, one is generated from experiment an another is from calculation using some curve fitting. I want two know the correlation (R2) value of this two sets of data.

Opening experiments on a smaller screen

Danobie — Fri, 14 Jun 2013 01:55:51 -0700

Hi all,

it would be nice if someone could help me with this problem:
I work on different computers with the same experiments but all of them are having different screen sizes. So sometimes some igor-windows disappear when I open the experiment on a computer with a smaller screen. They are just outside of the screen. Is there any command or function which pulls all the windows into the visible area again?

Thank you!

Danobie

Curvefit without adding the fit line to a graph?

yaohualiu — Thu, 13 Jun 2013 11:09:06 -0700

Hi,

Is there a flag to turn off automatically adding the fit to a graph?

Thanks,

Yaohua

Randomized Maze Generator using Prim's Algorithm

daggaz — Thu, 13 Jun 2013 07:30:53 -0700

Was fooling around today and decided to try this out, looks pretty cool as it builds the maze. Tips and tricks to improve my code design are very welcome!

#pragma rtGlobals=3		// Use modern global access method and strict wave access.
//PRIM's ALGORITHM: RANDOMIZED MAZE GENERATOR
//coded by Ian Allen, 13, June, 2013
 
 
function maze_maker(dim_x,dim_y)
variable dim_x, dim_y // maze dimensions, recommended to use odd values but even does work
 
//initiate the maze
make/o/d/n=(dim_x,dim_y) maze = 1
make/o/d/n=(dim_x,dim_y) cell_logic = 0
make/o/d/n=(1,4) wall_list = 0 // [x_coord,y_coord,delta_x,delta_y] delta is where to check for the adjacent cell
variable/g num_walls = 0
 
variable i
for(i=0;i<dim_x;i+=2)
	maze[i][] = 0
	maze[][i] = 0
endfor
//newimage cell_logic
newimage maze
dowindow/c/w=graph0 maze_win
 
 
//pick a seed cell to begin process
variable x_coord = floor((enoise(.4999) + .5)*((dim_x - 2)/2)) * 2 + 1
variable y_coord = floor((enoise(.4999) + .5)*((dim_y - 2)/2)) * 2 + 1
variable wall_num
print x_coord,y_coord
cell_logic[x_coord][y_coord] = 1
//add the walls to the list
maze_maker_add_walls(x_coord,y_coord,dim_x,dim_y)
	do
		//roll for a wall and check it
		wall_num = floor((enoise(.4999) + .5)*num_walls)
		maze_maker_check_wall(wall_num,dim_x,dim_y)
 
 
	while (num_walls > 0)				
end
 
//---subroutine 1----//
 
function maze_maker_add_walls(x_coord,y_coord, dim_x,dim_y)
variable x_coord,y_coord, dim_x,dim_y //x y coord are cell coordinates not wall coordinates
nvar num_walls
wave wall_list,maze
//add the walls to the list if they exist and are not edge walls
if ( x_coord -1 != 0 && maze[x_coord-1][y_coord] == 0)  // LEFT wall
	insertpoints 0,1, wall_list	
	wall_list[0][0] =  x_coord - 1	
	wall_list[0][1] = y_coord	
	wall_list[0][2] = -1	
	wall_list[0][3] = 0
	num_walls +=1
endif 
if ( x_coord + 1 != (dim_x -1) && maze[x_coord+1][y_coord] == 0) // RIGHT wall
	insertpoints 0,1, wall_list
	wall_list[0][0] =  x_coord + 1
	wall_list[0][1] = y_coord
	wall_list[0][2] = 1
	wall_list[0][3] = 0
	num_walls +=1
endif
if ( y_coord - 1 != 0 && maze[x_coord][y_coord -1] == 0) // TOP wall
	insertpoints 0,1, wall_list
	wall_list[0][0] =  x_coord 
	wall_list[0][1] = y_coord -1
	wall_list[0][2] = 0
	wall_list[0][3] = -1
	num_walls +=1
endif
if ( y_coord + 1 != (dim_y -1) && maze[x_coord][y_coord +1] ==0) // BOTTOM wall
	insertpoints 0,1, wall_list
	wall_list[0][0] =  x_coord
	wall_list[0][1] = y_coord + 1
	wall_list[0][2] = 0
	wall_list[0][3] = 1
	num_walls +=1
endif
print num_walls
end
 
//---subroutine2---//
 
function maze_maker_check_wall(wall_num,dim_x,dim_y)
variable wall_num,dim_x,dim_y
nvar num_walls
wave wall_list,cell_logic,maze
variable x_coord = wall_list[wall_num][0] // wall coordinates
variable y_coord = wall_list[wall_num][1]
variable new_x = x_coord + wall_list[wall_num][2]  // adjacent room coordinates
variable new_y = y_coord + wall_list[wall_num][3]
 
if (cell_logic[new_x][new_y] == 0)
	maze[x_coord][y_coord] = 1
	//insert update command here when you figure it out
	doupdate/w=maze_win
	cell_logic[new_x][new_y] = 1
	deletepoints (wall_num),1,wall_list
	num_walls -= 1
	maze_maker_add_walls(new_x,new_y, dim_x,dim_y)
else
	deletepoints (wall_num),1,wall_list
	num_walls -=1
endif
 
 
 
end

Surface plot using 2Dwave

jeps — Thu, 13 Jun 2013 06:14:45 -0700

Hi everyone,

I am trying to make a surface plot (please see attached file) with a 2Dwave, and two 1Dwaves. I have a matrix (Z) of dimension (9473,89), a "channel" (Y) wave of dimension (89), and a "time serie" (X) wave of dimension (9473).

when I type this in the command line:
Display;AppendImage Z vs {X,Y}
I get an error message saying that my X&Y waves don't have enough data points....
pretty weird. So after having added two points to both waves (now dimensions: 9474 and 90, respectively), it says that my X wave is not monotonic....

I don't really understand the errors, and don't see why I should add (create) useless datapoints that are not supposed to exist!

Does someone have any tip?
Thanks a lot!!

initiating multi-dimensional waves with zero rows

daggaz — Thu, 13 Jun 2013 05:49:50 -0700

For data management, it seems nice to create an empty wave to hold data and then add points as the data is created:

make/o/d/n=(0,3) data_wave
for (i = 0; i < cutoff_point ; i +=1)
   generate a,b,c,d
   insertpoints 0,1,data_wave
   data_wave[0][0] = a
   data_wave[0][1] = b
   data_wave[0][2] = c
   data_wave[0][3] = d
endfor

unfortunately, IGOR doesnt seem to recognize the second dimension unless there is at least one row (sigh, whats the point?)

Is there some clever trick you guys use to get around this, without doing something ugly like starting the first row = 0, and then remembering to always subtract one from the length of the wave for the rest of the code?

Or is that what we do?

surface plot I would like to do

jeps — Thu, 13 Jun 2013 06:14:46 -0700

Full width half maximum

raponzoni — Wed, 12 Jun 2013 13:47:35 -0700

Hi everyone!

I am really new at IGOR (I've watched all video tutorials, and know the basics), but I have a fundamental doubt: I am adjusting a peak of my experimental data using three peaks. How do I get the value of FWHM for the total peak and not just for each peak used?

Thanks in advance por helping?

Conflict sarfia neuromatic

eco_ri — Wed, 12 Jun 2013 05:58:22 -0700

I'm currently using Neuromatic for my data analysis, but since I install Sarfia, Igor is stuck in a message that says:
name already exist as a function
Error in NM_Utility.ipf:DeleteNANs
Function DeleteNANs(wList, yname, xflag)

If I delete the sarfia procedures everything goes normal.
I'm new at Igor and I have no clue in how to address this problem.
Thanks

Insert a graphic inside a graphic

raponzoni — Tue, 11 Jun 2013 06:12:32 -0700

Hi there,

I would like to insert a graphic (as pdf picture) inside a graphic, so I can show a zoomed part of it. I've watched again all the tutorials and made a search here but couldn't find anything like this. I was able to add the picture using the annotation tool, but I cannot resize it.
Is it possible?
Perhaps it's much more easy to use any image editor, but I like the quality of pdf graphics from IGOR :)

Attached is a picture of what I'm trying to do.

Many thanks

Correlation (R2) between two plots

tsaha — Wed, 12 Jun 2013 07:16:50 -0700

I have two sets of data of a particular experiment, one is experimental an another is calculated theoretically. I want to know the correlation factor (R2) of this two curves.

Avoiding copies of button on all tabs

fltcoils — Wed, 05 Jun 2013 14:04:15 -0700

Is there a way to create a new control on a tabbed panel and avoid it occuring on all the tabs?

I am working on a legacy interface, when I try to add a new control to the panel, it also appears on the other 2 panels (a 3 tabbed panel system). I'd like to have it exclusive to the middle panel.

Igor 6.2
win7

thanks

Errorbars and $string_with_wave_name

millot1 — Tue, 11 Jun 2013 13:23:44 -0700

I try to use errorbars in a generic fitting function that calls waves using $string_with_wave_name such as

display $Y_Wave_name vs  $X_Wave_name

(this is working)
However if I try to use

Errorbars $Y_Wave_name, XY wave=($XErr_Wave_name,$XErr_Wave_name),wave=($YErr_Wave_name,$YErr_Wave_name)

i have an error message saying that the trace is not on the graph.

I suspect a bug since if I use the same syntax with one particular set of names for X,Y Xerr and Yerr waves, Errorbars works fine

Error bars in Polar Plots

jjarrett64 — Tue, 11 Jun 2013 12:14:38 -0700

Dear all,

I am making some polar plots with data that has error bars, and I can't find a way to include them with the polar plots package.

Let's say I have data from 0 to 360 degrees in 20 degree intervals. Each point has an average value (plotted) and standard deviation that I want to plot as an error bar. Any ideas?

Any help figuring this out would be greatly appreciated.

Using CurveFit parameters in procedures

ali8 — Sun, 09 Jun 2013 14:40:28 -0700

Hi,

I am trying to implement this procedure:

#pragma rtGlobals=3	// Use modern global access method and strict wave access.
Function myAuto()
Wave Vx,i_t
Display Vx vs i_t
CurveFit/M=2/W=0 line, Vx/X=t/D
Make/N=50000/D fit
fit= W_coef[0]+W_coef[1]* i_t
Vx = Vx - fit
Save/T i_t,Vx,Vy as "aaa.itx"
End

The problem is in W_coeff, as Igor think they are "unkown/inappropriate". How can I modify it?

Recent posts by all users

matrix math: finding random solution

Category plot. Stroke color for error bars

graph

pre-triggered scanning

Loading spectroscopic data into igor from general text

how to display smoothing spline integration equation

Igor position at Oxford instruments, Asylum Research

Oxford Instruments

Shapiro Wilk test for Normality

Fitting curves erratic behavior?

Strange fitting curve

Correlation (R2) between two plots

Opening experiments on a smaller screen

Curvefit without adding the fit line to a graph?

Randomized Maze Generator using Prim's Algorithm

Surface plot using 2Dwave

initiating multi-dimensional waves with zero rows

surface plot I would like to do

Full width half maximum

Conflict sarfia neuromatic

Insert a graphic inside a graphic

Correlation (R2) between two plots

Avoiding copies of button on all tabs

Errorbars and $string_with_wave_name

Error bars in Polar Plots

Using CurveFit parameters in procedures