Recently Created Projects

LaTeX Pictures

JimProuty — Wed, 08 Feb 2012 17:28:32 -0800

The LaTeX Pictures.ipf procedure file implements a "LaTeX Pictures" panel which uses a web site to render LaTeX math equations into PNG bitmaps. Igor 6.20 or later is required.

This version generates only PNG pictures that can be drawn in Igor annotations and with DrawPICT (Igor's drawing tools).

This is mostly a proof-of-concept project that would be improved by finding or establishing an online LaTeX-to-PDF renderer to provide high-resolution equations.

See the "LaTeX Help" button in the panel and search online for "LaTeX math mode syntax" to learn what kinds of LaTeX commands will work with this implementation. (There are some quirks about extra backslashes to get the right number of backslashes through Igor's command language and all the way across the internet to the LaTex renderer.)

It is conceivable that in the future this panel can be extended to use PDF format for high resolution, if I can figure out how to generate a PDF that isn't tied to a page size. I know how LaTeXIt does it, and it doesn't look easy.

It does not require the installation of any LaTex-related software on your computer. I think this is actually quite a good thing.

The images are rendered by the (apparently free) "Roger's Online Equation Editor" at:

http://rogercortesi.com/eqn/index.php

Let me take this opportunity to recommend LaTeXIt for Macintosh. LaTeXIt gets the PDF sizing right, and has a terrific user interface:

http://www.chachatelier.fr/latexit/

Installation

The LaTeX Pictures.ipf procedure file should be moved to Igor's User Procedures folder, and used by placing

#include "LaTeX Pictures"

in your experiment's procedure window.

This adds a "LaTeX Pictures" item to Igor's "Misc" menu.

Size Distribution Fitting (lognormal) - Wdie-Range Particle Sizer (WPS) Data Processing

baroques_solari — Fri, 03 Feb 2012 00:21:18 -0800

This igor procedure is to handle the airborne particle size distribution data measured using Wdie-Range Particle Sizer (WPS), since the original software provided along with the instrument is not very user-friendly.

Starting with a neatly organized panel, all functions are simple and straightforward:
- Load raw data with a single click;
- Automatically obtain major parameters (RH, temperature) and calculate the hourly average; (daily or monthly average will be added in future release)
- Graphing (size distribution, color-coded by number conc.);
- Fit the size distribution into three log-normal modes (aitken/accumulation/coarse), using Lavenburg-Marquardt method.

Feel free to contact with me at wangsiyuan AT ust DOT hk.

Expt Procedures

bmcguyer — Thu, 15 Dec 2011 08:36:05 -0800

Template with an experiment file and several procedure files to help simplify data acquisition and management in Igor Pro. Includes generic data-taking routines, a convention for identifying data with unique serial numbers, procedure files to simplify data acquisition (see "DAQ Procedures" Project*) with GPIB, NIDAQ, serial port, and VISA, and procedure files to work with a few common SRS lockin amplifiers and Tektronix oscilloscopes. Each file contains its own documentation, and the experiment file contains a "GettingStarted" notebook.

Some of this template builds on "Alex Procedures," a very useful set of Igor Pro procedures written by Dr. Alex Johnson while working for Professor Charles Marcus at Harvard. "Alex Procedures" is documented in Appendix D of its author's Ph.D. dissertation, and is available online at:
http://marcuslab.harvard.edu/how_to/alexprocedures.zip
In particular, "Expt_Data.ipf" and "Expt_Analysis.ipf" were inspired by "alexdata.ipf" and "alexanalysis.ipf", and the "2D-Graph Profile Utility" of "Expt_Graph_Utilities.ipf" is based off a similar feature from "alexanalysis.ipf".
However, this template is not compatible with "Alex Procedures."

For example, "Expt_Data.ipf" provides the functions setval() and getval() to identify different experimental parameters with strings, so that functions like do1d() can sweep arbitrary parameters in order to produce a data set of one or more waves. "Expt_Analysis.ipf" provides conventions for do1d() to assign a unique serial number to the data set, and to archive useful information in the wavenotes of the data waves. This allows you to later use a serial number with shownum() to graph a data set with automatically labeled axes.

This template uses optional conditional computation (#if) to ease sharing between multiple computers. These statements require Igor Pro v6 or higher, and should be commented out for earlier versions.

*Link to "DAQ Procedures": http://www.igorexchange.com/project/DAQ_Procedures

DAQ Procedures

bmcguyer — Fri, 02 Dec 2011 14:01:59 -0800

Procedure files to help simplify data acquisition (DAQ) in Igor Pro. Includes separate files for GPIB, NIDAQmx, traditional NIDAQ, serial port, and VISA. Each file contains its own documentation.

For example, "DAQ_GPIB.ipf" provides generic functions for managing communication with multiple devices over GPIB, using a scheme for identifying devices with strings, and provides a control panel for troubleshooting GPIB issues. Similarly, "DAQ_NIDAQmx.ipf" (and "DAQ_NIDAQ_Traditional.ipf") provide generic functions for working with NIDAQ. "DAQ_SerialPort.ipf" provides routines for using one device over a serial port (RS-232), and is currently specialized for a particular Omega temperature controller. "DAQ_VISA.ipf" provide generic functions for working with the first device detected by VISA over USB.

These files are also available as part of the "Expt_Procedures" project: http://www.igorexchange.com/project/Expt_Procedures

User Function Profiling

Larry Hutchinson — Fri, 02 Dec 2011 10:36:16 -0800

The procedure file in this project will be in the WaveMetrics Procedures folder in 6.23 and provides a means of finding the bottlenecks in your user Function code. Until 6.23 is released, if you currently have a version of 6.20, you can try it out by downloading the most recent build of Igor here:
http://www.wavemetrics.net/Downloads/latest/

For this beta5 release, the Igor from the above page needs to be from a build date of Tue, 13 Dec 2011 or later.

This release supports ThreadSafe Functions and Functions contained in independent modules (but all code must execute in the main thread.) In addition to calling your test code via RunFuncWithProfiling as described below, you can start profiling, then start your test however you want and finally stop profiling. See the comments at the top of the procedure (renamed to FunctionProfiling.ipf in the beta2 release.)

To use the procedure, create a simple test function that takes no parameters and exercises your code for a least one second. Then, after loading the procedure, execute

RunFuncWithProfiling(YourTest)

The result will be a notebook containing annotated versions of the functions in your code that took the most time (top 80%.) Here is a simple example. Given:

Function Test()
	Variable i,imax=1000000
	for(i=0;i<imax;i+=1)
		Variable v1= 1
		Variable v2= sin(v1)
		Variable b3= enoise(1)
	endfor
End

Running

RunFuncWithProfiling(Test)

resulted in:

Top function percentages:
Function Procedure#Test: 100
 
Top functions with line annotations:
 
*******************************************************************************************
Function: Procedure#Test; Percent total 100
*******************************************************************************************
[00]          	|Function Test()
[00]          	|	Variable i,imax=1000000
[10]*         	|	for(i=0;i<imax;i+=1)
[11]*         	|		Variable v1= 1
[21]**        	|		Variable v2= sin(v1)
[49]*****     	|		Variable b3= enoise(1)
[08]*         	|	endfor
[00]          	|End

The procedure file, FunctionProfiling.ipf, contains comments at the top that provide more information on its use.

Ocean Optics XOP

741 — Mon, 07 Nov 2011 08:51:47 -0800

This XOP allows you to control and acquire data from Ocean Optics spectrometers.

We use it to acquire spectra from a USB2000+ spectrometer, but I believe that it should work for other spectrometers as well.

The download includes binaries and source code, and instructions on how to use the software.

NRFit

jhjcho — Fri, 28 Oct 2011 18:36:29 -0700

Neutron and X-ray reflectivity analysis package:

Use Parratt formalism

Simple and easy to use

Provide a number of functions for roughness

Installation:

Option1: Download anywhere on your computer and open_file/procedure from 'File' menu in IgorPro.

Option2: Download and copy it into Igor Procedures folder in IgorPro. It will shows up in the menu.

Note: if it complains about FONT, select your favorite font and apply it to all experiments. And new users might want to turn ON Tips from the Graph menu.

Downloads:

Download a proper version (window, mac) for you. (click "View all releases" below to see all the versions on NRFit page, especially for MAC with IgorPro <= 6.0.).

Links:

SANS analysis standalone software (WIN, MAC): SansView (http://danse.chem.utk.edu/sansview.html). Note: NR function can be found in the custom model type in the Fitting application.

Scattering Length Density Calculator (http://sld-calculator.appspot.com) : Google Webapp for PC, MAC, iPhone, and iPad.

...

Chemical Bonding Curves Demo

jjweimer — Tue, 11 Oct 2011 13:05:57 -0700

Overview

This demonstration experiment shows the shapes of curves for potential energy and force for seven expressions commonly used in chemical bonding. They include ionic, Born-Mayer, Mie, Morse, Buckingham, Lennard-Jones 6-12, and Hooke's Law. The potential is in a dimensionless form of U/Uo versus distance as r/ro, where Uo is the potential at equilibrium distance ro. Force is dimensionless by its maximum value Fmax.

Features

A control panel allows you to change the potential expression and vary the key parameters. A ClipIt button allows you to take a snapshot of the curves at a given set of parameters in order to compare to curves at other parameter settings.

Distribution Details

Experiments: Chemical Bond Curves.pxp
Procedure Files: none
XOPS: none
Requires Packages: NONE
Benefits From: NONE
Help Files: none
Documentation: internal notebook for the experiment demo

ColorScaleSliders

741 — Mon, 03 Oct 2011 09:51:28 -0700

ColorScaleSliders includes a single procedure file that lets you adjust the color scaling of false-color image plots using sliders. By combining smooth adjustments with immediate feedback, this helps you optimize the appearance of false-color plots, and allows you to find fine details.

ColorScaleSliders also includes a similar slider-driven approach to combining up to three different images into a single RGB image. A potential use could be the visualization of multicolor fluorescence data.

To use this procedure simply load the included .ipf file, open an image plot, and select "Append Colorscale Sliders" from the macros menu.

Kinetic Reaction Demo

jjweimer — Sat, 10 Sep 2011 10:08:35 -0700

Overview

This package is a demo that was created for a class in chemical kinetics. It illustrates the behavior of a chemical reaction network A <--> I --> P under various settings of rate constants, equilibrium conditions, and temperature.

Features

Use the checkboxes to turn on / off equilibrium of the first reaction and running the second reaction.

Use set variable inputs to change pre-factors, activation energies, and reaction enthalpy. Use a slider to set the equilibrium constant or reaction temperature.

Distribution Details

Experiments: KineticReactionDemo
Procedure Files: none
XOPS: none
Requires Packages: NONE*
Benefits From: NONE
Help Files: none
Documentation: internal notebook for the experiment demo

User Notes

The curves are calculated using a numerical integration routine. Sometimes, the code hangs (at least on my system). The source of this problem is under investigation.

LogBook

jjweimer — Mon, 11 Jul 2011 18:51:08 -0700

Overview

This provides a control panel to input systematic logbook information in to a notebook, including a header, a graphic (window or picture), notes, and a history reading. It also allows you to execute commands from the note field and capture the history.

The DEVELOPMENT SNAPSHOP (below) currently contains the latest bug fixes and features

Features

Use the checkboxes to turn on / off a header input, with a title, date, and time.

Use the popup to select the order to put a graphic object (none, 1, or 2). Select the graphic (or let it select dynamically via !), and define its format, frame, black/white, and size parameters.

Use the popup to select the order to put notes (none, 1, or 2). Erase the notes or autoclear them with each push to the notebook. Include dynamic codes # or % in the note field to run functions or get readouts.

Check whether to capture the history to the notebook either incrementally or accumulated.

Define what notebook to capture the log (or let it select dynamically via !). Set the location in the notebook (top, prior paragraph, current, next paragraph, or end).

Use special characters to invoke functions from within the note field. Any text preceded by # and ending in ) is run via Execute as a function. Any text preceded by % and ending in ) is taken as a call to a string function that inserts the return value at that point in the notes. Special commands %graphic(0) and %graphic(1) insert the name of the graphic and the traces on the graph, respectively.

Hit the button or type command+shift+= (Mac) or control+shift+= (Windows) to send the information to the notebook as a log.

With dynamic function calls (words prefaced by #) in the notes, the order of chunks defines what shows in the notebook. With the graphic placed first, any dynamic function calls get executed AFTER the graphic is captured. With the notes placed first, dynamic function calls in the note field get executed BEFORE the graphic is captured. The history is always captured last.

Example Dynamic Codes

%graphic(0) - places the name of the graphic at that point in the notes
%graphic(1) - places the names of the traces on a graph at that point in the notes
%date() - inserts the date at that point in the notes
%MyStringList(10) - inserts the string results from MyStringList(10) at that point in the notes
#print date() - prints the date to the history area
#MyFunction(10,3,5) - runs my function with the given parameters
#{MyOperation parameters} - runs my operation with the given parameters

Distribution Details

Experiments: none
Procedure Files: LogBook.ipf
XOPS: none
Demos: none
Requires Packages: NONE*
Benefits From:
Package Tools
ScreenSizer
Help Files: LogBook.ihf
Documentation: the Web pages for this project

User Notes

You MUST have Package Tools installed to remove this package properly. You SHOULD have Package Tools installed to get help and other information for the package.

Localizer - localization microscopy toolkit

741 — Wed, 20 Apr 2011 12:18:48 -0700

Localizer provides a full package for performing localization analysis in superresolution fluorescence microscopy (PALM, STORM). The package comes in two parts, an XOP that is responsible for performing fast and efficient calculations, and an Igor procedure that provides a graphical front-end.

The XOP includes operations for a full analysis, including:
* Native loading of data from the manufacturer's file format for a range of scientific cameras (currently Photometrics, Andor, Hamamatsu, some Zeiss .lsm files, and grayscale TIFF files).
* Highly accurate segmentation of low-intensity Gaussian-like emitters (i.e. fluorescent molecules) from a noisy, inhomogeneous background.
* Precise localization of emitters using a variety of different algorithms (user-selectable).
* Post-processing of the analysis result, e.g. drift correction or emitter blinking (implemented in the procedure)
* Different algorithms for producing publication-quality figures.
* Support for converting input data to different file formats, e.g. a standards-compliant TIFF file or Quicktime movie.

All operations have been designed to work with multi-gigabyte data that is much larger than the available computer memory.

A full reference on the operations implemented in the XOP is included with the package. This makes the XOP suitable for custom programming, possibly providing a convenient means for dealing with data from scientific cameras or as a powerful segmentation algorithm for recovering Gaussian-like emitters from grayscale images.

No programming experience is required to use this package.

Synchronized Windows

harneit — Tue, 15 Mar 2011 18:04:12 -0700

Igor supports exterior panels that stick to the target window, but only for graphs and panels.
SyncWin extends this idea to any pair of target windows (also tables, layouts, notebooks).
To use, create two windows and install the link between them using SyncWinInstall().
The following examples are also given in the procedure file.

Example 1:

string myGraph = "MyOtherGraph"
Display /N=$myGraph /W=(300,90,500,190)
Display /N=MyFirstGraph /W=(350,100,550,200)
SyncWinInstall(myGraph)

Example 2:

string myPanel = "Panel0", myTable = "Table0"
Edit /N=$myTable /W=(100,50,300,150)
NewPanel /N=$myPanel /W=(150,60,350,160)
SyncWinInstall(myPanel, mainWin = myTable, anchor = "LB", killmode = 1)

Example 3:

string myLayout = "Layout0", myNB = "NB0"
NewLayout /N=$myLayout /W=(200,70,400,170)
NewNotebook /F=1 /N=$myNB /W=(250,80,450,180)
SyncWinInstall(myNB, mainWin = myLayout, anchor = "TC", killmode = 2)

Sticky Notes

harneit — Sun, 06 Mar 2011 16:26:18 -0800

Just type away while your mouse is over a graph to create a "Sticky" (a.k.a. sticky note, or text box)

Usage:
1. Create a graph, bring it to the front.
2. Call InstallStickies() for the top graph window or choose "use stickies in top graph" from the Stickies menu.
3. Point the mouse somewhere inside the graph, start typing.
That's it.

Full documentation in the Procedure file.

Generic Window Hook

harneit — Sun, 06 Mar 2011 16:05:46 -0800

GenericWindowHook.ipf provides
1) a generic window hook function that monitors events, GenericWinHook(), and
2) an installer function, InstallGenericWinHook(), that sets up an exterior panel (dubbed here the "event panel") to show all monitored events.

- Works for any window that can receive events (Graphs, Tables, Layouts, Panels, Notebooks).
- You can simply use the event panel to examine what really happens to your window while developing your own hook function.
- You can also use the GenericWinHook() code as a starting point for own your hook function.

Usage:
- From the command line or from your own function, call InstallGenericWinHook() for the top window (Graph, Panel, Table, Layout, or Notebook).
- You can also provide a target window name (here: Table0) using the optional parameter syntax: InstallGenericWinHook(winName = "Table0").
- After that, watch what kind of events your target window is receiving in response to user actions (mouse, keyboard, menu, ...)

Full documentation is in the procedure file.

Fiber Composite Designer

jjweimer — Sun, 27 Feb 2011 15:24:52 -0800

Overview

This is a package that was developed to show how uniform, continuous, fiber composites behave using different input parameters. You can vary the densities, modulii, strengths, and fiber volume fraction. Graphs show the stress-strain behavior of the system, the intrinsic density or fiber weight fraction, and the iso-strain or iso-stress modulus or specific modulus of the composite. Everything is self-contained.

Visualization and Analysis of Broadband Transient Absorption Data

mysfeir — Fri, 11 Feb 2011 12:07:35 -0800

Chirp correction procedures have landed in version 4.2! Please email with any comments or bugs.

This package includes a set of functions for processing and graphing wavelength and time-resolved absorption data. This code was designed to process data created by the Helios Femtosecond Transient Absorption spectrometer produced by Ultrafast Systems, LLC. However, it will work with any data with the format:

0, time_1, time_2, . . . , time_M wavelength_1, deltaOD_1_1, deltaOD_1_2, . . . , deltaOD_1_M wavelength_2, deltaOD_2_1, deltaOD_2_2, . . ., , deltaOD_2_M . . . wavelength_N, deltaOD_N_1, deltaOD_N_2, . . ., , deltaOD_N_M

where N, M are arbitrary integers.

Please note: this procedure requires that the MultPeakFit extension be loaded into Igor. For instructions, see the Igor help files or refer to the attached documentation.

This package is being produced to assist our external Users and collaborators with their data analysis and visualization needs. Current functionality includes the ability to:

directly import *.csv files produced by data acquisition software and stores file info to the Igor notes area
process those files to remove NaNs, Infs, and extra padding
create waves in appropriate format for 2D image plots and 3D surface plots
allow for quick inspection of kinetic and spectral data using cursors placed on the image files
allow for easy extraction (single pixels or an average over an arbitrary range of pixels) and automatic plotting of 1D kinetic or spectral data
process data to remove scattered light under degenerate pump-probe conditions
extract a subset of data (region on interest) directly from an image plot using the cursors to bound the data
allow for easy time zero correction of matrix and kinetic data
generate a progressive time axis with arbitrary start and end points for use in acquisition software
provide a set of commonly used curve fitting functions for first and second order kinetics
provide a User-friendly and consistent interface to Igor's singular value decomposition and global fitting capabilities
chirp correction routines!

For instructions, please refer to the attached pdf documentation. This package is under active development, so check back soon!

For information about our Spectroscopy facility, please visit:

http://www.bnl.gov/cfn/facilities/Advanced_Optics.asp

To do list:

Rewrite curve fitting functions so that they can be used in conjunction with SVD analysis.
Integration of Fourier Transform routines for coherent phonon analysis.
DeltaA/A processing from linear spectra.

PicoHarp File Access for Igor Pro

mysfeir — Fri, 11 Feb 2011 11:24:36 -0800

This procedure is based on the File Access Demo in Matlab script written by Peter Kapusta, PicoQuant GmbH, September 2006.
It was ported to IGOR Pro so that the binary data files (*.phd) created by the PicoHarp 300 time correlated single photon counting module can be directly read and analyzed.

This procedure has been tested with version 2.0 of the PicoHarp file format (since Sept 2006) and is compatible with the most current hardware models.

This script adds a menu item, "Load PicoHarp *.phd File" to the Load Waves menu. It reads the contents of a *.phd file and writes all relevant experimental information to the IGOR history area. The data from each channel 0 - 7 is stored in a separate wave, scaled appropriately to the instrument resolution for that channel.
By default it produces a graph containing all waves plotted on a log y scale.

There are two versions of this procedure, one for IGOR Pro v.4+ and one for IGOR Pro v.6+.

For information about our spectroscopy facilities, please visit:

http://www.bnl.gov/cfn/facilities/Advanced_Optics.asp

MatrixFileReader XOP

thomas_braun — Mon, 31 Jan 2011 07:35:15 -0800

The MatrixFileReader XOP enables Igor Pro to read data acquired with the MATRIX Data acquisition system developed by Omicron Nanotechnology GmbH. The files are not interpreted directly, rather they are accessed through libraries from the Vernissage Toolkit by the same company.

Main Features

Very fast wave creation from a broad range of SPM/STS data types
Meta data conservation for a proper measurement documentation
No detour via the flat file format required
Check for recently acquired bricklets in the result file
Extensive documentation inside Igor
Works with data from all MATRIX versions
Possibility to access the raw untransformed data, therefore compatible with all matrix data types
The complete source code is available under a FLOSS license (LGPLv3 or later) for maximum flexibility and openness

Supported data acquisition modes (thoroughly tested)

Topography (Z and I)
Single Point Spectroscopy (Z and I)
Grid Spectroscopy (Z, I and varied-Z)
All Aux, Aux(V) channels

Due to lack of appropriate hardware, AFM data could not be tested. In case you can help with testing the AFM support, please contact me.

System Requirements

Windows XP SP2/Vista/7
Igor Pro 6.20 or later
Vernissage Toolkit 2.0/2.0-1 (only these two versions are supported), available from Omicron

Installation

Install Igor 6.20 or later
Start Igor, this will create a folder called WaveMetrics in "My Documents"
Install Vernissage 2.0/2.0-1
Install the shipped vcredist_x86.exe (Microsoft Visual C++ 2005 Redistributable Package x86).
Copy "matrixfilereader.xop" to "My Documents\WaveMetrics\Igor Pro 6 User Files\Igor extensions"
Copy "matrixfilereader Help.ihf" to "My Documents\WaveMetrics\Igor Pro 6 User Files\Igor Help files"
Restart Igor
Load the experiment matrixfilereader-basic-gui.pxp which includes a basic GUI for easy access to the XOP operations
Enjoy!

Bug Reports

In case you find a bug please create a new issue in the issue tracker below. Be sure to attach the output of the command MFR_GetReportTemplate and describe your problem.

Development

This XOP is considered feature complete, so only bugfix releases are planned. In case you have a working patch which implements a new feature don't hesitate to contact me.

pFLIM - an analysis program for time-domain fluorescence lifetime imaging microscopy (FLIM) data

KirstinWalther — Mon, 10 Jan 2011 09:01:27 -0800

We have developed a highly accurate and efficient code for the analysis of time-domain FLIM data (‘‘pFLIM’’ for precision FLIM). Our analysis code accounts for all significant instrumental artifacts (e.g., the instrument response function (IRF) and spatially inhomogeneous background events) and is rigorously based on both conventional and novel statistics. The code is described in detail in the manuscript:

Precise measurement of protein interacting fractions with fluorescence lifetime imaging microscopy, Walther et al., Mol. BioSyst., (2011), DOI: 10.1039/c0mb00132e
http://pubs.rsc.org/en/Content/ArticleLanding/2011/MB/C0MB00132E

If you use the code in a publication, please cite the above manuscript.

The package contains pFLIM.ipf, pFLIM.xop (one for PC, one for MacOSX), and a pdf file with detailed instructions on how to use the program. It uses two other packages available from the IgorExchange website:

multiopenfiles - http://www.igorexchange.com/project/multiopenfiles
TabControl - http://www.igorexchange.com/project/ACL_tabcontrol

The program currently only reads in FLIM data in the PicoQuant .pt3 file format. This can, however, be changed by modifying the XOP accordingly. If you are interested, contact me and I will provide you with the source code.