Igor

IgorPro is a powerful command-line based data analysis and plotting software. Asylum Research (our AFM manufacturer) uses Igor to control their AFMs. See also the Jimenez research group's Igor page for a quick reference.

Useful hotkeys:

• cntrl+j Quick switch to command line
• cntrl+i Adds cursor palette to a plot

Useful windows:

• The “data browser” window is helpful to keep track of the names of waves you are manipulating. Data > Data Browser.

Useful commands:

• To learn more about a command, write it at the command line, highlight it, right click and choose the help option.
• “edit data1, data2” creates a table with the waves data1 and data2
• “display data1 vs data2” Plots data1 vs data2
• “duplicate data1, data1copy” Creates a duplicate wave of data1 called data1copy
• “duplicate/R=[1502,7102] ithrom ithrom_short” Creates a duplicate wave that use a limited range of the original data.
• “DeletePoints startdatapoint, numberofdatapoints, data1” Deletes a specified number of datapoints starting at a specified datapoint.
• “Note data1, “some text”” Attaches some text as a note to a wave. Useful for storing informal comments relating to the wave
• “print note(data1)” Displays any notes associated with a wave
• SetAxis changes the x and y axes of a plot
  • SetAxis/A Automatically sets the x & y axes
  • SetAxis bottom 1,3 Sets the x-axis to the range 1 to 3
  • SetAxis left 1e-9,5e-9 Sets the y-axis to the range 1e-9 to 5e-9
• DeletePoints 50, 150, data Deletes 150 datapoints from data starting from datapoint 50
• “vgthrom_flat = vgthrom - p*0.00833333*0.21+2” The index p is used to define a line. In this example, the command was used to flatten some biosensing data.
• “duplicate/R=(0,11) vgflat vg30” The R stands for range. The coordinates refer to either the data point in the wave or the scaled x axis for the wave.
• “Smooth 60, vg100_smth” The smoothing window will be 60 data points. I already used the duplicate command to make a wave called vg100_smth.
• “Make/N=150/D Xb” This is like the Matlab command zeros(150), making a vector that has 150 entries of zero.
• “Xb = p” This makes a vector [0, 1, 2, 3, …]

Importing a data file to Igor:

Data>Load Waves>General Text

When importing current vs. time data, throw out the time column then change wave scaling (this can also be done with the SetScale command)

Data>Change wave scaling

Some automated functions which are useful for speedy analysis of switching data are contained in the following procedure file (download and unzip the file. Then double-click it to open it in Igor). These functions partially automate and speed up tasks like autocorrelation, Fourier analysis, Fourier filtering, plotting, etc. You can find a list of the functions, as well as instructions for calling them, in the procedure file's header.

• Select Windows→Help Windows→WM Procedures Index.ihf
• Press cntrl+f to open the search box in the help window. Search for 'PSD'.
• Press the include icon (spiral bound notebook) next to the 'Power Spectral Density' section
• A text will open, hide the text
• From now on a 'PowerSpectralDensity' macro will be available in the Macros pull down menu.

We have a copy of a macro that Asylum Research wrote for taking PSDs over long times (showing lower frequency information). The procedure file for this is located at: T:\Physics\Minot Group\Software\Igor Pro\BigPSD.ipf

• Navigate to /WaveMetrics/Igor Pro Folder/More Extensions/File Loaders/
• Create shortcuts for 'SndLoadSaveWave.xop' and 'LoadWAVfile.xop'
• Move the shortcut files to /Wavemetrics/Igor Pro Folder/Igor Extensions/

• Create a 16 bit audio wave in Igor

Make/W/O/N = NumberOfDatapoints WaveName

• Set the sample rate (=1/tau) for the wave

SetScale/P x,0,0,tau, WaveName

• Copy time domain data into the audio wave. You will need to choose a scaling factor to multiply your data by (otherwise the resulting sound wave will be too loud or quiet). For a 16 bit sound wave values between -32768 and 32767 are allowed. Pick a scaling value that puts your data comfortably in that range.

WaveName = DataWave*ScaleFactor

* Listen to your new audio file

PlaySound WaveName