====== 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 [[http://cires.colorado.edu/jimenez-group/wiki/index.php/Igor_Quick_Reference|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
==== Procedures for analysis of switching data ====
Some automated functions which are useful for speedy analysis of switching data are contained in the following {{::LandonsProc.zip|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.

==== Power Spectral Density ====
== PSD preparation ==
  *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.

== Big PSD preparation ==
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
==== Working with audio files ====
== Preparation (only necessary on first use) ==
  *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/

== Making an audio file from ASCII data ==
  * 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