Computer Code for Materials Scientists: Igor Pro Procedures for Analyzing Dynamic Light

Computer Code for Materials Scientists: Igor Pro Procedures for

Analyzing Dynamic Light Scattering, Rheology, and Synchrotron

X-ray Scattering Data

Adam K. Schmitt1,* and Mahesh K. Mahanthappa

1

1Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706

*Corresponding Author: Email [email protected].

Table of Contents

Abstract ......................................................................................................................................................... 2

Introduction ................................................................................................................................................... 2

Acknowledgments ......................................................................................................................................... 3

Procedure Explanations ................................................................................................................................ 3

DLS_Toolbar ............................................................................................................................................ 3

Rheology ................................................................................................................................................... 4

Sec5Tools .................................................................................................................................................. 4

Sec12Tools ................................................................................................................................................ 5

References ..................................................................................................................................................... 6

Procedure Help Files ..................................................................................................................................... 6

DLS_Toolbar ............................................................................................................................................ 6

Rheology ................................................................................................................................................... 8

Sec5Tools .................................................................................................................................................. 9

Sec12Tools .............................................................................................................................................. 11

Procedures ................................................................................................................................................... 14

DLS_Toolbar .......................................................................................................................................... 14

Rheology ................................................................................................................................................. 35

Sec5Tools ................................................................................................................................................ 40

Sec12Tools .............................................................................................................................................. 61

mailto:[email protected]

Abstract

The development of modern tools for rapidly screening the structures and properties of designer materials

for various technological applications mandates the development of new methods for quickly and

conveniently reducing, analyzing, and visualizing complex data sets to enable their meaningful

interpretation in multidimensional parameter spaces. Toward this end, procedures were written for use

with Igor Pro (Wavemetrics, Inc.) that allow fast data reduction and analysis for common Materials

Science characterization experiments. These techniques include dynamic light scattering (DLS), torsional

rheology, and synchrotron small- and wide-angle X-ray scattering (SAXS and WAXS, respectively). For

these experiments, the volume of data and complexity associated with its analysis in real-time are often

cumbersome to researchers. These procedures were written to assist and to enable the loading,

visualization, and analysis or interpretation of data in an effort to render tedious data analyses faster and

more convenient.

Introduction

Routine materials sample characterization quickly becomes tedious as the number of samples increases or

as the depth and complexity of the data analysis increases (e.g., multivariable fits). The following

procedures were written to ease this burden and to enable the reduction and complex analysis of data from

various techniques commonly used in advanced materials characterization. These procedures specifically

assist in the analysis of raw experimental data from dynamic light scattering, torsional rheology, and

synchrotron X-ray scattering. The research in our group primarily focuses on the morphological

properties of soft materials, including block copolymer melts and solutions,1-2

and polymer blends, and

lyotropic liquid crystalline phases of small molecule surfactants in water and in non-aqueous media.3 All

of these research projects necessitate quantitative structural characterization at various length scales,

ranging from ~ 1-100 nm. These properties may be probed by the above techniques, yet the data reduction

and analysis can be non-trivial in some cases.

These procedures are written for Igor Pro (Wavemetrics, Inc.), which allows for very high levels of end-

user customization in the way a program operates. Each of the procedures described herein consist of

three parts: (1) data loading, (2) visualization, and (3) analysis or interpretation. One very convenient

feature of these procedures is the ability to batch load files for processing by importing an entire file

directory. This eliminates the tedious sequential data loading that is usually associated with large data

sets. These programs also readily enable data visualization, which is critical for its interpretation.

Because the data analysis in each procedure differs slightly due to differences in the experimental

technique and the desired output and interpretation, a brief explanation of the capabilities of each analysis

routine follows.

The DLS_Toolbar is used to analyze dynamic light scattering data; specifically, it requires a .fit

file as input that is generated by a Brookhaven BI-9000AT digital autocorrelator. This procedure

can perform fits to different functional forms (single/double exponential decay) depending on the

system of interest. The diffusion coefficient and the hydrodynamic radius of one or more

populations in solution can be determined along with cumulants to analyze the population

dispersity.

The Rheology procedure is used to plot and to analyze data generated from a dynamic

temperature frequency sweep test; it requires that the data be collected and exported using the TA

Instruments Orchestrator software. This test in conjunction with the time-temperature

superposition principle allows for the determination of storage and loss moduli data at

experimentally inaccessible frequencies through the generation of master curves.

The Sec5Tools procedure analyzes small-angle X-ray scattering data from Sector 5 (DND-CAT)

at the Advanced Photon Source at Argonne National Laboratory (Argonne, IL). The procedure

allows for batch data loading, customizable visualization (e.g., overlay and stacked plots, option

for Kratky plot), and assistance in indexing scattering patterns through the addition of powder

diffraction peak indicators characteristic of commonly observed crystallographic symmetries.

The Sec12Tools procedure is used to analyze small- and wide-angle X-ray scattering from Sector

12 (12-ID-B) at the Advanced Photon Source at Argonne National Laboratory. The procedure

allows for batch data loading, customizable visualization (e.g., overlay and stacked plots, SAXS,

WAXS or SWAXS plots), and advanced data analysis including powder diffraction peak position

markers and conversion to file formats that are compatible with commonly used crystallographic

analysis programs.

Acknowledgments

The authors acknowledge financial support from University of Wisconsin-Madison and a National

Science Foundation CAREER Award (DMR-0748503) to M.K.M. We also acknowledge access to the

DuPont-Northwestern-Dow Collaborative Access Team 5-ID-D beam line and 12-ID-B beamlines at the

Advanced Photon Source at Argonne National Laboratory (Argonne, IL). The DuPont-Northwestern-Dow

Collaborative Access Team beamline (Sector 5), which is supported by E. I. DuPont de Nemours & Co.,

the Dow Chemical Company, the State of Illinois, and the U.S. Department of Energy, Office of Basic

Energy Sciences (Contract No. DE-AC02-06CH11357). The Chemical & Materials Science beamline

(Sector 12) is supported by the U.S. Department of Energy, Office of Basic Energy Sciences (Contract

No. DE-AC02-06CH11357).

Procedure Explanations

DLS_Toolbar

The DLS_Toolbar procedure is designed to analyze Dynamic Light Scattering (DLS) data acquired using

a Brookhaven Instruments DLS system (Brookhaven BI-9000AT digital autocorrelator). In a DLS

experiment, the fluctuating scattered light intensity is measured as a function of time and scattered angle.

These time-dependent fluctuations are then transformed into an autocorrelation function, which provides

insight into the time scales of the fluctuations, and thus, the diffusion of the particles in solution. The

autocorrelation function can be fit to different functional forms to determine the particle diffusion, which

can be related to the hydrodynamic radius of the particle using the Stokes-Einstein relation.4

This procedure takes as input a .fit file, which is the output from the autocorrelator. This file has a four-

row header and consists of three columns: time (s), measured intensity, and fitted intensity. This

procedure uses only the first two columns. After the data has been loaded, the autocorrelation function

can be fit to one of four built-in functions (single exponential, single exponential with cumulant, double

exponential, and double exponential with cumulant).4 Each of these functions applies to a specific

colloidal system of interest, subject to various simplifying assumptions. If you are unsure of which

function to use, please see the help file for this procedure.

This procedure also has the function to perform multi-angle light-scattering fits. After fitting all data

corresponding to a single sample at multiple detector angles, the resulting data can be compiled into a

multi-angle plot to determine more accurately the diffusion coefficient and the hydrodynamic radius

according to the Stokes-Einstein relation.4

Rheology

The Rheology procedure enables the analysis and generation of master curves from the time-temperature

superposition of temperature- and frequency-dependent rheological data. This procedure is compatible

with data acquired using TA Instruments ARES rheometers operated by the TA Orchestrator software.

Torsional Dynamic Mechanical Analysis (DMA) of a sample encompasses a wide variety of different

sample testing modes (isothermal frequency sweeps, isochronal temperature sweeps, and dynamic strain

sweeps). One very useful and comprehensive test is a dynamic frequency/temperature sweep test, the

results of which may be interpreted in the context of the time-temperature superposition principle (TTS).

TTS relies on the principle of corresponding states, such that a measurement at a specific frequency and

temperature can be related to another measurement at a slower frequency and lower temperature.5

When a dynamic temperature/frequency sweep is performed, isothermal frequency sweeps are measured

over a range of user-specified temperatures. Shift factors are applied to each of the various isothermal

frequency sweep data sets to align them with a single reference data set at a selected reference

temperature. This shifted data comprises a master curve, which shows the extended frequency behavior of

the sample. Further analysis, beyond the scope of this program, facilitates the determination of the

activation free energy of flow of the sample based on these shift factors.

This procedure takes as input the raw, unshifted data (Dynamic Frequency Temperature Sweep test data)

and the shift factors from the TA Orchestrator software. The data are separated by temperature and shifted

using the shift factors exported from the TA Orchestrator software. Additionally, it is possible to edit the

shift factors in order to obtain a better fit and to apply these modified shift factors to the plotted data. The

procedure allows for multiple plotting options of the resulting master curve and shift factors allowing for

the determination of the Williams-Landel-Ferry (WLF) parameters.5

Sec5Tools

The Sec5Tools procedure is used for reducing, visualizing, and analyzing small-angle X-ray scattering

(SAXS) data acquired at the 5-ID-D beamline (DND-CAT) at the Advanced Photon Source (APS) at

Argonne National Laboratory (Argonne, IL). SAXS is a useful tool for quantitatively interrogating the

morphology and principal domain spacing of a material. The observed scattering maxima in azimuthally-

integrated SAXS patterns can often be indexed to commonly-observed structures that are well known

(lamellae, the double gyroid, hexagonally-packed cylinders, and spheres packed on a body-centered cubic

lattice).6 The high flux at the APS allows for rapid analyses of a large volume of samples due to the short

X-ray exposure times required for high-resolution data acquisition, leading to the generation of very large

data sets in short periods of time. Furthermore, it is often necessary to analyze these giant data sets in

real-time in order to efficiently plan subsequent experiments and to minimize squandered experiment

time. This procedure offers a convenient way to import, organize, visualize, and index the patterns to

known morphologies facilitating real-time data analysis and planning at the beam line.

This procedure takes as input the large data sets often generated at Sector 5 at the APS. The files consist

of many data types, but the critical files for this procedure are the processed plot files containing intensity

(I(q)) versus scattering vector (q) data in addition to other relevant data. The typical filenames generated

at the beamline consist of user initials and a scan number. It is critical to keep good records of which scan

number corresponds to each sample and data acquisition temperature. To tag these data sets in a

meaningful manner, a comma separated text file (no spaces) must be generated that lists scan number,

sample name, exposure temperature and the number of scans (averaged). This text file is also an input for

the procedure.

After the text file is loaded, the entire directory of data can be loaded in a single user operation (see

procedure help file for more information). The scans may then be plotted on separate graphs or together in

stacked or overlayed configurations. In order to analyze the data, powder diffraction peak position

markers corresponding to four typical morphologies (lamellae, double gyroid, hexagonally-packed

cylinders, and spheres packed on a cubic lattice) can be overlayed on the azimuthally-integrated data to

determine the sample morphology.

Sec12Tools

The Sec12Tools procedure is used for reducing, visualizing, analyzing small- and wide-angle X-ray

scattering data (SWAXS) acquired at the Sector 12 beamline (12-ID-B) at the APS. SWAXS is used in

the same manner as SAXS (above) with the added benefit of being able to study phenomena that occur on

length scales ranging from ~1-50 nm (e.g., surfactant self-assembly, crystallization). As in SAXS (see

Sec5Tools), the positions of the observed scattering peaks and their associated scattering intensities may

be used to determine the underlying crystallographic space group symmetry of the nanostructured

material. In conjunction with other crystallographic software packages (JANA2006,7 Superflip,

8 and

VESTA9), one can perform Rietveld refinements of the X-ray data and construct electron density contrast

maps. Again, the amount of data generated during experimental runs at this beam line is overwhelming,

and this procedure provides a convenient means of importing, organizing, visualizing and interpreting the

data.

This procedure takes as input the large data sets generated at Sector 12, which are comprised of scattered

intensity (I(q)) versus scattering wavevector (q) data in addition to other relevant data. In contrast to the

data acquisition interface at the 5-ID-D beamline, the Sector 12 data station allows the user to define

custom filenames for each sample exposure. The entire directory of data is loaded in one user operation

and is available for subsequent use from a drop-down menu. The data can be plotted as described above

to display the SAXS data, the WAXS data, or both (SWAXS). Powder diffraction peak position indicator

lines may be overlayed to assist with morphological assignments. These lines can also be directly

converted to peak markers, facilitating quick export of publication quality figures. Additionally, in the

case of very complicated scattering patterns that do not index to the typically observed morphologies, the

azimuthally integrated SAXS pattern can be converted from I(q) vs. q to I(q) vs. 2θ and the intensity

scaled (relative intensity to “Counts”) for compatibility with the crystallographic software package Jade

(Materials Data, Inc.). Jade may then be used to determine the space group and refine the structure of the

sample.

References

1. L. Leibler, Theory of Microphase Separation in Block Copolymers. Macromolecules 1980, 13, 1602-

1617.

2. F. S. Bates, G. H. Fredrickson, Block Copolymers---Designer Soft Materials. Physics Today 1999,

52, 32-38.

3. T. Kato, N. Mizoshita, K. Kishimoto, Functional Liquid-Crystalline Assemblies: Self-Organized Soft

Materials. Angewandte Chemie International Edition 2006, 45, 38-68.

4. W. F. Edmonds, M. A. Hillmyer, T. P. Lodge, Block Copolymer Vesicles in Liquid CO2.

Macromolecules 2007, 40, 4917-4923.

5. P. C. Hiemenz, T. P. Lodge, Polymer Chemistry 2nd Edition. CRC Press: Boca Raton, FL, 2007.

6. S. Förster, A. Timmann, M. Konrad, C. Schellbach, A. Meyer, S. S. Funari, P. Mulvaney, R. Knott,

Scattering Curves of Ordered Mesoscopic Materials. The Journal of Physical Chemistry B 2005, 109,

1347-1360.

7. V. Petricek, M. Dusek, L. Palatinus, Jana2006. The crystallographic computing system. Institute of

Physics: Praha, Czech Republic, 2006.

8. L. Palatinus, G. Chapuis, SUPERFLIP - a computer program for the solution of crystal structures by

charge flipping in arbitrary dimensions. J. Appl. Cryst. 2007, 40, 786-790.

9. K. Momma, F. Izumi, VESTA: a three-dimensional visualization system for electronic and structural

analysis. J. Appl. Cryst. 2008, 41, 653-658.

Procedure Help Files

DLS_Toolbar

• Help File for DLS_Toolbar

DLS_Toolbar procedure and help file written by Adam K. Schmitt.

This procedure is used to import, plot, and fit autocorrelation functions generated by Brookhaven

Instruments Dynamic Light Scattering instruments. This procedure contains many different fit-functions

and can also fit multi-angle data.

• Loading DLS data into Igor

This procedure was designed to import .fit files generated by a Brookhaven BI-9000AT digital

autocorrelator. To load DLS data, select Tools > DLS > "Load and Graph" or "Load and Graph All".

"Load and Graph" enables examination of specific data sets in a folder containing many different

measurements. "Load and Graph All" is useful when you have a folder of the same sample measured at

different detector angles. To use "Load and Graph", simply select the data file you seek to open. To use

"Load and Graph All", select the directory containing the files you wish to open.

• Changing default parameters

If you are running experiments under non-standard conditions, you may select "Open and Set Parameters"

to change the default values for temperature (°C), wavelength (WL in nm), solvent refractive index (RI),

and solvent viscosity (Pa·s). The default conditions for this procedure are experiments in water at 25°C (T

= 298.15 K, WL = 532 nm, RI of solvent = 1.333, solvent viscosity = .001 Pa·s). These values are used

later in calculating the diffusion coefficient and hydrodynamic radius.

• Included fit-functions

There are four fit-functions included in this procedure file for fitting the observed autocorrelation

function. These include Single Exponential (SE), Single Exponential with Cumulant (SEWC), Double

Exponential (DE), and Double Exponential with Cumulant (DEWC). SE should be used for

measurements of monodisperse particles. If your solution contains a polydisperse mixture of particles that

exhibit a unimodal size distribution, SEWC should be used. If there are two populations of particles in

solution that exhibit different sizes, yet the two populations are narrowly dispersed, DE should be used. If

you have a mixture of two polydisperse populations, DEWC should be used. When using a cumulant fit,

the dispersity can be calculated as dispersity = /2.

If you do not know what is in solution, as is sometimes the case, you should work your way through the

fit functions in order of increasing complexity: SE, SEWC, DE, DEWC.

• Fitting autocorrelation functions

After you have loaded the data, set the default parameters, and decided which fit-function is most

appropriate for your sample, you are ready to start fitting your data. First, select the plot that you would

like to fit, then select “Fit Data” followed by the desired fit function. This will bring up a dialog to control

the fitting. The fitting equation is displayed on the top-right of the dialog. Use the slider bars to adjust the

values of the parameters to be used as the initial guess for fitting. Complex data fits sensitively depend on

good initial guesses to obtain accurate fits quickly. This procedure allows you to alter the parameters and

see the effect they have on the fit. Move the sliders until the fit line overlays almost exactly over the data.

If any of the parameters cannot reach the necessary value or if the value is too low on the slider bar, you

can adjust the sensitivity. To adjust the sensitivity, move the slider to the maximum value (to the right)

then click either "Up" or "Down" to increase or decrease the maximum value for that slider by a factor of

10. Once the initial guess lines up very nicely with the data, you can submit the initial guess and start the

fit by selecting the "Start Fit" button. You will be prompted to enter the detector angle (in degrees) of the

measurement. This allows for multi-angle plots and fitting later. Once you enter this value, the plot and fit

are shown along with the diffusion coefficient and hydrodynamic radius calculated using the Stokes-

Einstein relation.

• Multi-angle plots

After you have fit DLS data associated with all of the different measured angles for a given sample, you

may combine the data and perform a multi-angle plot. To do this, select "Multi-Angle Plot". This brings

up a small dialog box to ensure that you have analyzed all of the measurements at different angles. If you

have fitted your data, select "Start". This will bring up another dialog. Here, you should select the

different angles that you wish to use. You must use a minimum of two and up to a maximum of five

angles. Use the drop-down boxes to select the different angular data. NOTE: The procedure automatically

generates a wave specifically used to combine multiple angles into one plot. These waves will be names

based on the measurement angle and the fit function used (e.g., single exponential fit at 60° is named

60SE). Select the correct waves using the drop-down boxes being sure to put the waves in order from

smallest angle to largest angle. Once you have selected your data, select "_none_" on the remaining boxes

to remove them from evaluation, then select "Continue". This brings up the multi-angle data plot and fit,

which furnishes the diffusion coefficient and hydrodynamic radius calculated from the Stokes-Einstein

relation.

Rheology

• Help File for Rheology Procedure

Rheology procedure and help file written by Adam K. Schmitt.

This procedure is used to import data from time-temperature superpositions in TA Orchestrator (TA

Instruments, Inc.) to Igor Pro for plotting figures and adjusting shift factors.

• Working up files in TA Orchestrator

Open the Dynamic Frequency Temperature Sweep file in TA Orchestrator. The first step is to separate the

sweeps from each other. To do this, select Tools > Freq/Temp Sweep Separation in Orchestrator and

select Frequency. This will create many windows each with a frequency sweep at a different temperature.

To start the TTS session, select TTS > Select Data to Shift. Now, select all of the Freq. Sweep files,

choose the lowest temperature sweep as the "Reference Experiment Set" and press "Next > >". Now press

"Create TTS". This brings up two windows. On the left is the TTS data unshifted and on the right are the

shift factors at the different temperatures. To shift the data, select TTS > Shift All Data Sets. This

automatically determines the best fit shift factors and applies them to the data, to generate the Master

Curve, now shown on the left.

• Exporting files from TA Orchestrator

To export the files, select the right window and go to File > Export. Enter a suitable name at the dialog for

the .rad file generate, such as SampleShifts.rad. Now, select the original window containing the unshifted

data (the Dynamic Frequency Temperature Sweep data) and do the same, this time with a name such as

SampleTTS.rad. These are the files that need to be imported into Igor. NOTE: You cannot export the

shifted data sets in a usable form–you must export the original unshifted data.

• Loading files into Igor

Now the files that were just exported need to be imported into Igor. To do this, in Igor select Tools >

Rheology > Load TTS, Shift and Plot. This will bring up a dialog to select a file. Be sure to choose the

.rad file with the unshifted data from the Dynamic Frequency Temperature Sweep experiment. The next

dialog to appear is a renaming dialog box. Since the file names are typically complicated, this dialog box

allows the user to rename them with much simpler names. The final dialog is for importing the shift factor

.rad file.

Now the Master Curve is plotted for the storage modulus, G`. Also, the shift factors are shown in the table

for each different temperature.

• Modifying/updating shift factors

At this point, you can manually change the shift factors to try to obtain a better data fit. If you change the

values in the table, the graph will not update automatically. To update the graph, select Tools > Rheology

> Update Shifts. This will replot the newly shifted data. You can iteratively alter the shifts, until you

obtain a satisfactory fit.

• Plotting master curves

You can plot Master Curves of the shifted data by selecting Tools > Rheology > Plot Master Curve. You

are then prompted to choose between plotting only the Storage Modulus (G'), only the Loss Modulus (G'')

or both G’ and G”.

• Plotting shift factors

It is also convenient to show the shift factors at each temperature, allowing for the quantitative

determination of the Williams-Landel-Ferry (WLF) parameters. By selecting Tools > Rheology > Plot

Shift Factors, you can display an Arrhenius-type double y-plot with the horizontal shift factors plotted on

the left axis in a log scale and the vertical shift factors plotted on the right axis in a linear scale against

Temperature plotted on the horizontal axis.

Sec5Tools

• Help File for SAXS-APS-5

SAXS-APS-5 procedure and help file written by Adam K. Schmitt.

This procedure imports SAXS data taken at Sector 5-ID-D at the APS at Argonne National Lab (Argonne,

IL). It loads entire directories of files generated at the beamline and provides a convenient way to

visualize and to interpret the data rapidly and in real-time.

• Launching SAXS-APS-5 Panel

To launch the panel, select Tools > SAXS > Sector 5 > Sector 5 Tools. This will open the APSToolKit

panel, which allows access to all the functions in this procedure.

• Loading data into Igor

To load the SAXS data taken at Sector 5, there must be an accompanying info file generated by hand to

correlate the scan numbers to sample names and scan temperatures. This info file is a text file consisting

of four comma separated columns, those being Scan Number, Sample Name, Temperature, and Number

of Scans. There should be no spaces in this file and each scan number should be on a separate line.

NOTE: Not all scan numbers will need to be listed in this file, since dark scans also have scan numbers

that are not used for samples and thus not included in the imported data.

This file is then loaded into Igor by selecting "Load Info File" under the "Load Data Files" section at the

top of the panel. Pressing this button brings up a dialog to select the .txt info file.

The next step is to import the actual data files into Igor. It is easiest to import all the files at once using the

"Load Directory of Files" option. It is also possible to load only a single file using "Load One File". The

files that need to be loaded are located by searching for the "processing" folder in the SAXS data

generated at Sector 5. Inside this folder will be a list of folders containing different user folders. Select the

folder containing your data. This folder should contain a folder called "plot_files". This folder contains

the files that need to be imported into Igor. Select "Load Directory of Files" and navigate to the

aforementioned folder. You should see the files being loaded in the Command window. At this point, you

can either load other folders of data (by going back to the user folder list and selecting a different folder

containing another "plot_files" folder) or you may start plotting the data. NOTE: If the number of scans

for a sample is greater than one, the procedure selects the correct averaged file to import. Only use the

"Load One File" option if you are very familiar with the file output at Sector 5. NOTE: If you try to

import any other folder (besides plot_files), the files will not load and you will not be able to use the other

functions contained in this procedure.

• Plotting data

The plotting functions included in this procedure are diverse and allow for a high level of end-user

customization of the final plots generated. To start, select the wave you would like to plot from the

"Select Wave to Plot" drop-down menu. This menu contains a list of all of the scans that have been

imported into Igor. NOTE: If this drop-down menu simply says "_error_", no files have been loaded or

the file loading was performed incorrectly. To fix this problem, return to the previous section of the help

file and try to reload the files.

After you have selected the wave you wish to plot, you must ensure that the plotting options that follow

are correct. Under "Select Operation", select "Create New Graph" if you would like to start a new graph,

select "Append to Top Graph" if you would like to add this trace to a pre-existing graph that is currently

the highest (at the top), and select "Remove from Top Graph" if you would like to remove the selected

wave from the top most graph. NOTE: If there are no graphs created yet, "Append to Top Graph" and

"Remove from Top Graph" will have no effect. Also, if the selected wave is not on the top graph,

"Remove from Top Graph" will have no effect.

Under "Select Plot Style" there are two options. "Overlay plot" will plot multiple files on top of each

other and will not apply any offsets to additional waves that are appended to the graph. "Stacked Plot"

will apply the necessary vertical offsets so the data is not overlapping and can be visualized with ease.

NOTE: If the data have drastically differing intensities (disordered versus strongly microphase separated),

the offsets will not be sufficient to prevent overlapping traces.

Under "Select Plot Type" there are two options. You can either plot the log(I(q)) vs. q for a conventional

SAXS plot or you can plot the log(I(q)·q2) vs. q for a Kratky-type plot.

After the options have been correctly set, click the button to apply the changes. NOTE: This button will

say "Plot New!" if you are creating a new graph, "Append!" if you are appending the wave to the top

graph, or "Remove!" if you are removing the wave from the top graph.

Continue using these options to create stacked or overlayed plots containing multiple samples or

temperature sweeps.

• Interpreting data using powder diffraction peak position markers

Powder diffraction peak position markers are a useful way to identify morphologies in block copolymers

and lyotropic liquid crystals. This procedure includes functions for lamellar, hexagonal, spherical and

gyroid phases. To utilize the powder diffraction peak markers, select the wave that you want to index

using the "Select Wave to Plot" drop-down menu, then press the "Add Diffraction Lines" button. This

will bring up two new windows. The first window, titled "difflinesplot", is the I(q) vs. q plot of the wave

selected, and the second is the panel controlling the diffraction lines, titled "Add Diffraction Lines". To

display the powder diffraction peak position markers for a particular morphology, click the check box to

the left of the morphology name on the right side of the panel. In cases where the primary peak is the

most intense point on the plot, the procedure automatically finds the q-value of the primary reflection and

the diffraction markers should line up with the observed scattering peaks if the morphology is correct. In

the case where the scattering near the beam stop is more intense than your primary peak, you may have to

move the slider bar to the left of the morphology to select the proper q-value of the primary. NOTE: It is

possible to identify phase coexistence using this procedure. To do this, simply select both morphologies

present in the sample and set each to the corresponding q-value of the primary peak for each morphology.

When finished, make sure the plot is the top graph, and press the "Close" button on the panel. This will

close the "Add Diffraction Lines" panel and will rename the "difflinesplot" panel so as to not interfere

with future diffraction line plots. NOTE: If you close the "difflinesplot" window early or it is not the top

graph when "Close" is pressed, you will receive error messages during subsequent attempts to add

diffraction lines.

• Performing background subtraction

It is possible to perform background corrections with this procedure. To do this, you must select the

sample wave using the "Select Wave to Plot" drop-down menu. Then, select your background wave using

the "Select Background Wave" drop-down menu. NOTE: This background subtraction function is very

simple and does not apply any scaling factors. It will simply subtract the "background" wave from the

"sample" wave. To perform the background subtraction, press the "Subtract" button. The sample and

background traces are plotted in red (sample) and black (background) on the top half of the graph. On the

bottom half, the resulting background corrected trace is plotted in blue. These new background corrected

files are stored in a folder called "BackCorr" in the Igor file system. To get to these files using the data

browser, first navigate to the APS folder, then to the sample that you performed the background

subtraction on, then "BackCorr". The two files are "bci..." and "bcq..." and are the I(q) and q-value waves

respectively.

Sec12Tools

• Help File for SAXS-APS-12

SAXS-APS-12 procedure and help file written by Adam K. Schmitt.

This procedure is used to load, visualize and interpret X-ray scattering data collected at Sector 12-ID-B at

the APS at Argonne National Lab.

• Loading data

The easiest way to load the data generated at Sector 12 is to use the "Load Directory" option. It is also

possible to only import select files using the "Load One File" option, yet this is much less convenient for

large groups of data. When you select "Load Directory", you will need to pick the folder to load. This

folder is the "Averaged" folder located inside both the "SAXS" and "WAXS" folders. NOTE: If you

simply choose the "SAXS" or "WAXS" folders, no files will be loaded. The best practice is to load both

the SAXS and WAXS files generated at Sector 12 in order to view the largest possible q-range (range of

characteristic length scales).

After both SAXS and WAXS data sets are loaded using the "Load Directory" option, the data needs to be

combined to form the SWAXS data sets. The SWAXS data sets contain both the SAXS and WAXS

waves in an individual wave, which are useful for plotting both later in the process. To combine the data,

simply press the "Combine Data" button.

• Plotting data

The myriad plotting functions included in this procedure allow for a high level; of user customization of

the final plots generated. To get started, select the wave you would like to plot from the "Select Wave to

Plot" drop-down menu. In this menu are listed all of the scans that have been imported into Igor. NOTE:

If this drop-down menu simply says "_error_", no files have been loaded or the file loading was

performed incorrectly. To fix this problem, return the previous section of the help file and try to reload the

files.

After you have selected the wave you wish to plot, you must ensure that the plotting options that follow

are set correctly. Under "Select Operation", select "Create New Graph" to start a new graph, select

"Append to Top Graph" to add this trace to a pre-existing graph that is currently the highest (at the top),

and select "Remove from Top Graph" to remove the selected wave from the top most graph. NOTE: If

there are no graphs created yet, "Append to Top Graph" and "Remove from Top Graph" will have no

effect. Also, if the selected wave is not on the top graph, "Remove from Top Graph" will have no effect.

Under "Select Plot Style" there are two options. "Overlay plot" will plot multiple files on top of each

other and will not apply any offsets to additional waves that are appended to the graph. "Stacked Plot"

will apply the necessary offsets so the data is not overlapping and can be visualized with ease. NOTE: If

the data have dramatically different intensities (disordered versus strongly microphase separated), the

offsets will be insufficient to prevent overlapping traces.

Under "Select Which to Plot" there are three options. You can plot either only the "SAXS" or the

"WAXS" or you can plot the combined files by selecting "SWAXS",

After the options have been correctly set, click the button to apply the change. NOTE: This button will

say "Plot" if you are creating a new graph, "Append" if you are appending the wave to the top graph, or

"Remove" if you are removing the wave from the top graph.

Continue using these options to create stacked or overlayed plots containing multiple samples or

temperature sweeps.

• Converting data

This function is meant to simplify the export of data from Igor to Jade by converting from I(q) vs. q data

to I(q) vs. 2θ and modulating the intensity (from a relative intensity to “counts”), so that Jade (Materials

Data, Inc.) can read the file with sufficient resolution.

To convert a file for use in Jade, select the file using the "Select Wave to Plot" drop-down menu and press

the "Convert" button. This will briefly create a new table with converted values and will also bring up a

dialog. Navigate to where you would like to save the converted file and choose a suitable name. Upon

completion, the windows will disappear, yet the converted file will be saved in the specified location.

Because the beam energy is fixed at 12 keV at Sector 12, the conversion should work for all data taken at

this beamline. The q-values are converted to 2 data according to 2 = 180°/* sin-1

(1.033

Angstroms*q/4/).

• Adding powder diffraction peak markers to plots

Powder diffraction peak position markers are a useful way to identify morphologies in block copolymers

and lyotropic liquid crystals. This procedure includes functions for lamellar, hexagonal, spherical and

gyroid phases. To utilize the powder diffraction peak markers, select the wave that you want to index

using the "Select Wave to Plot" drop-down menu, then press the "Add Lines" button.

This will bring up two new windows. The first window, titled "difflinesplot", is the I(q) vs. q plot of the

wave selected, and the second is the panel controlling the powder diffraction peak position markers, titled

"Add Diffraction Lines". To display the powder diffraction markers for a particular morphology, click the

check box to the left of the morphology name on the right side of the panel. In cases where the primary

peak is the most intense point on the plot, the procedure automatically finds the q-value of the primary

and the diffraction peak markers should line up with the observed scattering peaks if the morphology is

correct. In the case where scattering near the beam stop is more intense than the primary peak, you may

have to move the slider bar to select the corresponding q-value of the peak. If your primary peak is out of

the range of the slider bars, you can use the "Low limit" and High limit" controls at the bottom of the

panel to adjust the range until you can accurately pinpoint the q-value of your primary scattering peak.

NOTE: It is possible to identify phase coexistence using this procedure. To do this, simply select both

morphologies present in the sample and set each to the corresponding q-value of the primary peak for

each morphology.

If you want to create markers on the plot in place of the vertical lines for use in figures, do not use the

"Close" button. Instead, make sure the "difflinesplot" is the top graph and press the "Markers" button.

This will bring up a dialog where you can enter the number of peaks you want indexed for each

morphology. NOTE: Only use a non-zero number of peaks if you want the peaks of that morphology to

be indexed on the plot. Typically, this means only one box is non-zero excluding cases with phase

coexistence. Finish the process by selecting "Continue" and the vertical lines will be converted to the

corresponding number of peaks for the morphologies selected.

If you do not want to add markers to the plot, make sure the plot is the top graph, and then press the

"Close" button on the panel. This will close the "Add Diffraction Lines" panel and will rename the

"difflinesplot" panel so as to not interfere with future diffraction line plots. NOTE: If you close the

"difflinesplot" window early or it is not the top graph when "Close" is pressed, you will receive error

messages during subsequent attempts to add diffraction lines.

Procedures

DLS_Toolbar

#pragma rtGlobals=1 // Use modern global access method.

// DLS Toolbar by AKS, 20130204

// This procedure is intended to be used to workup Dynamic Light Scattering data taken on a Brookhaven

Instruments multi-angle light scattering instrument using a Brookhaven BI-9000AT digital autocorrelator.

// This proceudre was developed by Adam K. Schmitt

Menu "Tools"

Submenu "DLS"

"Load and Graph All", LoadAndGraphAllDLS("")

"Load and Graph", LoadAndGraphDLS("","")

"Open and Set Parameters", ChangePar()

Submenu "Fit Data"

"SingleExponential", SingleExp2()

"Single Exponential with Cumulant", SingleExpWCum2()

"Single Exponential with Cumulant [g']", SingleExpWCumG()

"Double Exponential", DoubleExp2()

"Double Exponential with Cumulant", DoubleExpWCum2()

End

"Multi-Angle Plot", multipleAnglePlot()

End

End

// This function sets global parameters that are used throughout data workup

Function setVars()

// These variables are temperature, wavelength, refractive index of solvent, and viscosity of solvent

Variable/G gT = 298.15 // in K

Variable/G gWL=532 // in nm

Variable/G gRI=1.333

Variable/G gETA=.001 // in Pa s

End

// This function allows for changes to the default parameters

Function ChangePar()

NVAR gT

if (!NVAR_Exists(gT))

setVars()

endif

NVAR gT

NVAR gWL

NVAR gRI

NVAR gETA

NewPanel /W=(100,100,260,280)/K=1 as "Parameters"

TitleBox info1, pos={5,5}, title="Change Parameters and", frame=0

TitleBox info2, pos={5,30}, title="keep this window open", frame=0

SetVariable temp, pos={5,60}, limits={250,400,1}, value=gT, bodyWidth=120

SetVariable wavelen, pos={5,90}, limits={300,700,1}, value=gWL, bodyWidth=120

SetVariable ri, pos={5,120}, limits={0,4,.01}, value=gRI, bodyWidth=120

SetVariable eta, pos={5,150}, limits={.00001,.1,1}, value=gETA, bodyWidth=120

End

// This section defines the used functions and allows fits to data

Function SingleExpMy(w,x):FitFunc

Wave w

Variable x

return w[0]*exp(-2*w[1]*x)

End

Function SingleExpWCumMy(w,x):FitFunc

Wave w

Variable x

return w[0]*exp(-2*w[1]*x)*(1+w[2]*x^2/2)^2

End

Function SingleExpWCumGMy(w,x):FitFunc

Wave w

Variable x

return w[0]*exp(-w[1]*x)*(1+w[2]*x^2/2)

End

Function DoubleExpMy(w,x):FitFunc

Wave w

Variable x

return (w[0]*exp(-w[1]*x)+w[2]*exp(-w[3]*x))^2

End

Function DoubleExpWCumMy(w,x):FitFunc

Wave w

Variable x

return (w[0]*exp(-w[1]*x)*(1+w[2]*x^2/2)+w[3]*exp(-w[4]*x)*(1+w[5]*x^2/2))^2

End

Function LineThroughZero(w,x):FitFunc

Wave w

Variable x

return w[0]*x

End

// Function for loading data

Function LoadAndGraphAllDLS(pathName)

String pathName // Name of symbolic path or "" to get dialog

String fileName

Variable index=0

if (strlen(pathName)==0) // If no path specified, create one

NewPath/O temporaryPath // This will put up a dialog

if (V_flag != 0)

return -1 // User cancelled

endif

pathName = "temporaryPath"

endif

do // Loop through each file in folder

fileName = IndexedFile($pathName, index, ".fit")

if (strlen(fileName) == 0) // No more files?

break // Break

out of loop

endif

//start load and append to graph code

Display/K=1 //Create new graph

String name1 = fileName[0,strlen(fileName)-5]

String sxw, syw

sxw = name1+"0"

syw = name1+"1"

if(exists(sxw))

KillWaves $sxw,$syw

endif

LoadWave/N=$name1/J/D/K=0/L={3,4,0,0,2}/P=$pathName fileName

Wave xw = $sxw // Create wave references.

Wave yw = $syw

xw=xw/1000000

AppendToGraph yw vs xw

ModifyGraph log(bottom)=1

//end load and graph code

index +=1

while (1)

if (Exists("temporaryPath")) // Kill temp path if it exists

KillPath temporaryPath

endif

NVAR gT


ChangePar()

endif

return 0 // Signifies success.

End

Function LoadAndGraphDLS(fileName, pathName) // Load only one file

String pathName

String fileName

Display/K=1 //Create new graph

LoadWave/N=$fileName/J/D/K=0/L={3,4,0,0,2}/P=$pathName fileName

String name1 = S_fileName[0,strlen(S_fileName)-5] // Remove file suffix from name

String sxw, syw, sxw2, syw2

sxw = StringFromList(0,S_waveNames) // Get wave names

syw = StringFromList(1,S_waveNames)

sxw2=name1+"0" // Create new

wave names

syw2=name1+"1"

if (WaveExists(sxw2))

KillWaves sxw2,syw2 // Kill if they exist

endif

Rename $sxw, $sxw2 //Rename waves

Rename $syw, $syw2

Wave xw = $sxw2 // Create wave

references.

Wave yw = $syw2

xw=xw/1000000

AppendToGraph yw vs xw

ModifyGraph log(bottom)=1

NVAR gT


ChangePar()

endif


End

// Functions for fitting data to a single exponential function and extracting relevant data

Function SingleExp2()

Variable A,B

NewPanel /W=(100,100,500,260) as "Initial Guess for Fit"

TitleBox titleA, pos={5,5}, title="A=", frame=0

TitleBox titleB, pos={5,80}, title="B=", frame=0

Slider slideA, limits={0,.5,0}, pos={5,20}, size={200,50}, vert=0, ticks=1, variable=A,

proc=updateSingleExp

Slider slideB, limits={0,100000,0}, pos={5,95}, size={200,50}, vert=0, ticks=1, variable=B,

proc=updateSingleExp

Button senAup, pos={210,20}, title="Up", proc=updateSingleExpBut

Button senAdown, pos={210,40}, title="Down", proc=updateSingleExpBut

Button senBup, pos={210,95}, title="Up",proc=updateSingleExpBut

Button senBdown, pos={210,115}, title="Down", proc=updateSingleExpBut

TitleBox sens, pos={210,5}, title="Sensitivity", frame=0

TitleBox valA, pos={20,5}, title=num2str(A), frame=0

TitleBox valB, pos={20,80}, title=num2str(B), frame=0

TitleBox equation, pos={280,5}, title="f(t)=A*exp(-2*B*t)", frame=0

Button start, pos={280,55}, size={100,50},proc=startSingleExpFit, title="Start Fit"

End

Function updateSingleExpBut(ctrl): ButtonControl

String ctrl

Variable maxv

if (cmpstr(ctrl,"senAup")==0)

ControlInfo slideA; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideA, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senAdown")==0)


if(maxv==0)

maxv=1

endif

Slider slideA, limits={0,maxv/10,0}

endif

if (cmpstr(ctrl,"senBup")==0)

ControlInfo slideB; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideB, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senBdown")==0)


if(maxv==0)

maxv=1

endif

Slider slideB, limits={0,maxv/10,0}

endif

End

Function startSingleExpFit(ctrl): ButtonControl

String ctrl

String tempFit

NVAR gT


setVars()

endif

tempFit="tempFit"

//single fit function

if(exists(tempFit))

RemoveFromGraph tempFit

KillWaves tempFit

endif

Variable angle

Prompt angle, "Detector Angle in Degrees: "

DoPrompt "Experimental Paramters", angle

String xw, yw

xw=StringFromList(0,WaveList("*", ";","WIN:"))

yw=StringFromList(1,WaveList("*", ";","WIN:"))

if (WaveExists(cwave))

KillWaves cwave

endif

Make/N=2 cwave

ControlInfo slideA; cwave[0]=V_Value

ControlInfo slideB; cwave[1]=V_Value

DoWindow /K $WinName(0,64)

FuncFit/Q/NTHR=0 SingleExpMy cwave $yw /X=$xw /D

Variable A,B,q,D,R

NVAR gWL

NVAR gRI

NVAR gT

NVAR gETA

A=cwave[0]

B=cwave[1]

q=4*Pi*gRI/(gWL*10^-9)*sin(angle*Pi/360)

D=B/q^2

R=1.3806503*10^-23/6/Pi/D*gT/gETA

String texty = num2str(angle)+"º\r\rD ="+num2str(D)+" m\S2\M/s\rR\\Bh\\M

="+num2str(1000000000*R)+" nm"

TextBox/C/N=text0/F=0/A=RT texty

//end single fit function

ModifyGraph mirror=2,fSize=12,axThick=1.5,prescaleExp(left)=3,prescaleExp(bottom)=6;DelayUpdate

Label left "\Z14\F'Symbol'G\S(2)\M\Z14(t) - 1";DelayUpdate

Label bottom "\\Z16\\F'Symbol't(m\\F'Arial's)"

String name1= num2str(angle)+"SE"

Make $name1 = {q,B,D,R}

End

Function updateSingleExp(ctrl,ctrlVal,event): SliderControl

String ctrl

Variable ctrlVal,event

String xVals, tempFit

tempFit="tempFit"

Variable A,B

ControlInfo slideA; A=V_Value

ControlInfo slideB; B=V_Value

TitleBox valA, title=num2str(A)

TitleBox valB, title=num2str(B)

xVals = StringFromList(0,WaveList("*", ";","WIN:"))

if (exists(tempfit))


KillWaves tempFit

endif

Duplicate $xVals, $tempFit

Wave xs = $xVals

Wave fit = $tempFit

fit=A*exp(-2*B*xs)

Rename fit, tempfit

AppendToGraph fit vs xs

End

// Functions for fitting data to a single exponential function with a cumulant expansion and extracting relevant data

Function SingleExpWCum2()

Variable A,B,C




TitleBox titleC, pos={5,155}, title="C=", frame=0


proc=updateSingleExpWCum



Slider slideC, limits={0,1000000000,0}, pos={5,170}, size={200,50}, vert=0, ticks=1, variable=C,


Button senAup, pos={210,20}, title="Up", proc=updateSingleExpWCumBut

Button senAdown, pos={210,40}, title="Down", proc=updateSingleExpWCumBut

Button senBup, pos={210,95}, title="Up",proc=updateSingleExpWCumBut

Button senBdown, pos={210,115}, title="Down", proc=updateSingleExpWCumBut

Button senCup, pos={210,170}, title="Up",proc=updateSingleExpWCumBut

Button senCdown, pos={210,190}, title="Down", proc=updateSingleExpWCumBut




TitleBox valC, pos={20,155}, title=num2str(C), frame=0

TitleBox titleVarian, pos={280,40}, title="Variance=", frame=0

TitleBox valVarian, pos={335,40}, title=num2str(C/B^2), frame=0

TitleBox equation, pos={280,5}, title="f(t)=A*exp(-B*t)*(1+C*t^2/2)", frame=0

Button start, pos={280,90}, size={100,50},proc=startSingleExpWCumFit, title="Start Fit"

End

Function updateSingleExpWCumBut(ctrl): ButtonControl

String ctrl

Variable maxv



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif

if (cmpstr(ctrl,"senCup")==0)

ControlInfo slideC; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideC, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senCdown")==0)


if(maxv==0)

maxv=1

endif

Slider slideC, limits={0,maxv/10,0}

endif

End

Function startSingleExpWCumFit(ctrl): ButtonControl

String ctrl

String tempFit

NVAR gT


setVars()

endif

tempFit="tempFit"


if(exists(tempFit))


KillWaves tempFit

endif

Variable angle



String xw, yw




KillWaves cwave

endif

Make/N=3 cwave



ControlInfo slideC; cwave[2]=V_Value


FuncFit/Q/NTHR=0 SingleExpWCumMy cwave $yw /X=$xw /D

Variable A,B,C,varian,q,D,R

NVAR gWL

NVAR gRI

NVAR gT

NVAR gETA

A=cwave[0]

B=cwave[1]

C=cwave[2]

varian=C/B^2


D=B/q^2

R=1.3806503*10^-23/6/Pi/D*gT/gETA

String texty = num2str(angle)+"º\rD ="+num2str(D)+" m\S2\M/s\rR\\Bh\\M

="+num2str(1000000000*R)+" nm\r\\F'Symbol's\\F'Arial' ="+num2str(varian)






String name1= num2str(angle)+"SEWC"


End

Function updateSingleExpWCum(ctrl,ctrlVal,event): SliderControl

String ctrl



tempFit="tempFit"

Variable A,B,C



ControlInfo slideC; C=V_Value



TitleBox valC, title=num2str(C)

TitleBox valVarian, title=num2str(C/B^2)




KillWaves tempFit

endif


Wave xs = $xVals

Wave fit = $tempFit

fit=A*exp(-2*B*xs)*(1+C*xs^2/2)^2

Rename fit, tempfit


End

// Functions for fitting data to a single exponential function with cumulant expansion (G) and extracting relevant

data

Function SingleExpWCumG()

Variable A,B,C




TitleBox titleC, pos={5,155}, title="C=", frame=0


proc=updateSingleExpWCumG



Slider slideC, limits={0,1000000000,0}, pos={5,170}, size={200,50}, vert=0, ticks=1, variable=C,


Button senAup, pos={210,20}, title="Up", proc=updateSingleExpWCumGBut

Button senAdown, pos={210,40}, title="Down", proc=updateSingleExpWCumGBut

Button senBup, pos={210,95}, title="Up",proc=updateSingleExpWCumGBut

Button senBdown, pos={210,115}, title="Down", proc=updateSingleExpWCumGBut

Button senCup, pos={210,170}, title="Up",proc=updateSingleExpWCumGBut

Button senCdown, pos={210,190}, title="Down", proc=updateSingleExpWCumGBut




TitleBox valC, pos={20,155}, title=num2str(C), frame=0

TitleBox titleVarian, pos={280,40}, title="Variance=", frame=0

TitleBox valVarian, pos={335,40}, title=num2str(C/B^2), frame=0

TitleBox equation, pos={280,5}, title="f(t)=A*exp(-2*B*t)*(1+C*t^2/2)^2", frame=0

Button start, pos={280,90}, size={100,50},proc=startSingleExpWCumGFit, title="Start Fit"

End

Function updateSingleExpWCumGBut(ctrl): ButtonControl

String ctrl

Variable maxv



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif

if (cmpstr(ctrl,"senCup")==0)


if(maxv==0)

maxv=1

endif

Slider slideC, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senCdown")==0)


if(maxv==0)

maxv=1

endif

Slider slideC, limits={0,maxv/10,0}

endif

End

Function startSingleExpWCumGFit(ctrl): ButtonControl

String ctrl

String tempFit

NVAR gT


setVars()

endif

tempFit="tempFit"


if(exists(tempFit))


KillWaves tempFit

endif

Variable angle



String xw, yw




KillWaves cwave

endif

Make/N=3 cwave



ControlInfo slideC; cwave[2]=V_Value


FuncFit/Q/NTHR=0 SingleExpWCumGMy cwave $yw /X=$xw /D

Variable A,B,C,varian,q,D,R

NVAR gWL

NVAR gRI

NVAR gT

NVAR gETA

A=cwave[0]

B=cwave[1]

C=cwave[2]

varian=C/B^2


D=B/q^2

R=1.3806503*10^-23/6/Pi/D*gT/gETA

String texty = num2str(angle)+"º\rD ="+num2str(D)+" m\S2\M/s\rR\\Bh\\M

="+num2str(1000000000*R)+" nm\r\\F'Symbol's\\F'Arial' ="+num2str(varian)






String name1= num2str(angle)+"SEWCG"


End

Function updateSingleExpWCumG(ctrl,ctrlVal,event): SliderControl

String ctrl



tempFit="tempFit"

Variable A,B,C







TitleBox valVarian, title=num2str(C/B^2)




KillWaves tempFit

endif


Wave xs = $xVals

Wave fit = $tempFit

fit=A*exp(-B*xs)*(1+C*xs^2/2)

Rename fit, tempfit


End

// Functions for fitting data to a double exponential function and extracting relevant data

Function DoubleExp2()

Variable A1,B1,A2,B2


TitleBox titleA1, pos={5,5}, title="A1=", frame=0

TitleBox titleB1, pos={5,80}, title="B1=", frame=0



Slider slideA1, limits={0,.5,0}, pos={5,20}, size={200,50}, vert=0, ticks=1, variable=A1,

proc=updateDoubleExp

Slider slideB1, limits={0,100000,0}, pos={5,95}, size={200,50}, vert=0, ticks=1, variable=B1,






Button senA1up, pos={210,20}, title="Up", proc=updateDoubleExpBut

Button senA1down, pos={210,40}, title="Down", proc=updateDoubleExpBut

Button senB1up, pos={210,95}, title="Up",proc=updateDoubleExpBut

Button senB1down, pos={210,115}, title="Down", proc=updateDoubleExpBut

Button senA2up, pos={475,20}, title="Up", proc=updateDoubleExpBut

Button senA2down, pos={475,40}, title="Down", proc=updateDoubleExpBut

Button senB2up, pos={475,95}, title="Up",proc=updateDoubleExpBut

Button senB2down, pos={475,115}, title="Down", proc=updateDoubleExpBut

TitleBox sens1, pos={210,5}, title="Sensitivity", frame=0


TitleBox valA1, pos={25,5}, title=num2str(A1), frame=0

TitleBox valB1, pos={25,80}, title=num2str(B1), frame=0



TitleBox equation, pos={120,170},title="f(t)=(A1*exp(-B1*t)+A2*exp(-B2*t))^2", frame=0

Button start, pos={5,157}, size={100,50},proc=startDoubleExpFit, title="Start Fit"

End

Function updateDoubleExpBut(ctrl): ButtonControl

String ctrl

Variable maxv

if (cmpstr(ctrl,"senA1up")==0)

ControlInfo slideA1; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideA1, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senA1down")==0)


if(maxv==0)

maxv=1

endif

Slider slideA1, limits={0,maxv/10,0}

endif

if (cmpstr(ctrl,"senB1up")==0)

ControlInfo slideB1; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideB1, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senB1down")==0)


if(maxv==0)

maxv=1

endif

Slider slideB1, limits={0,maxv/10,0}

endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif

End

Function startDoubleExpFit(ctrl): ButtonControl

String ctrl

String tempFit

NVAR gT


setVars()

endif

tempFit="tempFit"


if(exists(tempFit))


KillWaves tempFit

endif

Variable angle



String xw, yw




KillWaves cwave

endif

Make/N=4 cwave

ControlInfo slideA1; cwave[0]=V_Value

ControlInfo slideB1; cwave[1]=V_Value




FuncFit/Q/NTHR=0 DoubleExpMy cwave $yw /X=$xw /D

Variable A1,B1,A2,B2,q,D1,R1,D2,R2

NVAR gWL

NVAR gRI

NVAR gT

NVAR gETA

A1=cwave[0]

B1=cwave[1]

A1=cwave[2]

B2=cwave[3]


D1=B1/q^2

R1=1.3806503*10^-23/6/Pi/D1*gT/gETA

D2=B2/q^2

R2=1.3806503*10^-23/6/Pi/D2*gT/gETA

String texty = num2str(angle)+"º\r\rD1 ="+num2str(D1)+" m\S2\M/s\rR\\Bh\\M1

="+num2str(1000000000*R1)+" nm\r\rD2 ="+num2str(D2)+" m\S2\M/s\rR\\Bh\\M2

="+num2str(1000000000*R2)+"nm"






String name1= num2str(angle)+"DE"

Make $name1 = {q,B1,D1,R1,B2,D2,R2}

End

Function updateDoubleExp(ctrl,ctrlVal,event): SliderControl

String ctrl



tempFit="tempFit"

Variable A1,B1,A2,B2

ControlInfo slideA1; A1=V_Value

ControlInfo slideB1; B1=V_Value



TitleBox valA1, title=num2str(A1)

TitleBox valB1, title=num2str(B1)






KillWaves tempFit

endif


Wave xs = $xVals

Wave fit = $tempFit

fit=(A1*exp(-B1*xs)+A2*exp(-B2*xs))^2

Rename fit, tempfit


End

// Functions for fitting data to a double exponential function with cumulant expansions and extracting relevant data

Function DoubleExpWCum2()

Variable A1,B1,C1,A2,B2,C2




TitleBox titleC1, pos={5,156}, title="C1=", frame=0


proc=updateDoubleExpWCum



Slider slideC1, limits={0,1000000000,0}, pos={5,170}, size={200,50}, vert=0, ticks=1, variable=C1,


Button senA1up, pos={210,20}, title="Up", proc=updateDoubleExpWCumBut

Button senA1down, pos={210,40}, title="Down", proc=updateDoubleExpWCumBut

Button senB1up, pos={210,95}, title="Up",proc=updateDoubleExpWCumBut

Button senB1down, pos={210,115}, title="Down", proc=updateDoubleExpWCumBut

Button senC1up, pos={210,170}, title="Up",proc=updateDoubleExpWCumBut

Button senC1down, pos={210,190}, title="Down", proc=updateDoubleExpWCumBut




TitleBox valC1, pos={25,156}, title=num2str(C1), frame=0

TitleBox titleVarian1, pos={120,230}, title="Variance1=", frame=0

TitleBox valVarian1, pos={175,230}, title=num2str(C1/B1^2), frame=0



TitleBox titleC2, pos={265,156}, title="C2=", frame=0





Slider slideC2, limits={0,1000000000,0}, pos={265,170}, size={200,50}, vert=0, ticks=1, variable=C2,


Button senA2up, pos={475,20}, title="Up", proc=updateDoubleExpWCumBut

Button senA2down, pos={475,40}, title="Down", proc=updateDoubleExpWCumBut

Button senB2up, pos={475,95}, title="Up",proc=updateDoubleExpWCumBut

Button senB2down, pos={475,115}, title="Down", proc=updateDoubleExpWCumBut

Button senC2up, pos={475,170}, title="Up",proc=updateDoubleExpWCumBut

Button senC2down, pos={475,190}, title="Down", proc=updateDoubleExpWCumBut




TitleBox valC2, pos={285,156}, title=num2str(C2), frame=0

TitleBox titleVarian2, pos={340,230}, title="Variance2=", frame=0

TitleBox valVarian2, pos={395,230}, title=num2str(C2/B2^2), frame=0

TitleBox equation, pos={120,260}, title="f(t)=(A1*exp(-B1*t)*(1+C1*t^2/2)+A2*exp(-

B2*t)*(1+C2*t^2/2))^2", frame=0

Button start, pos={5,230}, size={100,50},proc=startDoubleExpWCumFit, title="Start Fit"

End

Function updateDoubleExpWCumBut(ctrl): ButtonControl

String ctrl

Variable maxv



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif

if (cmpstr(ctrl,"senC1up")==0)

ControlInfo slideC1; maxv=V_Value

if(maxv==0)

maxv=1

endif

Slider slideC1, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senC1down")==0)


if(maxv==0)

maxv=1

endif

Slider slideC1, limits={0,maxv/10,0}

endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif



if(maxv==0)

maxv=1

endif


endif

if (cmpstr(ctrl,"senC2up")==0)


if(maxv==0)

maxv=1

endif

Slider slideC2, limits={0,maxv*10,0}

endif

if (cmpstr(ctrl,"senC2down")==0)


if(maxv==0)

maxv=1

endif

Slider slideC2, limits={0,maxv/10,0}

endif

End

Function startDoubleExpWCumFit(ctrl): ButtonControl

String ctrl

String tempFit

NVAR gT


setVars()

endif

tempFit="tempFit"


if(exists(tempFit))


KillWaves tempFit

endif

Variable angle,A1,B1,C1,A2,B2,C2,varian1,varian2,q,D1,D2,R1,R2

NVAR gWL

NVAR gRI

NVAR gT

NVAR gETA



String xw, yw




KillWaves cwave

endif

Make/N=6 cwave



ControlInfo slideC1; cwave[2]=V_Value



ControlInfo slideC2; cwave[5]=V_Value


FuncFit/Q/NTHR=0 DoubleExpWCumMy cwave $yw /X=$xw /D

A1=cwave[0]

B1=cwave[1]

C1=cwave[2]

A2=cwave[3]

B2=cwave[4]

C2=cwave[5]

varian1=C1/B1^2

varian2=C2/B2^2


D1=B1/q^2

R1=1.3806503*10^-23/6/Pi/D1*gT/gETA

D2=B2/q^2

R2=1.3806503*10^-23/6/Pi/D2*gT/gETA

String texty = num2str(angle)+"º\r\rD1 ="+num2str(D1)+" m\S2\M/s\rR\\Bh\\M1

="+num2str(1000000000*R1)+" nm\r\\F'Symbol's\\F'Arial'1 ="+num2str(varian1)+"\r\rD2 ="+num2str(D2)+"

m\S2\M/s\rR\\Bh\\M2 ="+num2str(1000000000*R2)+" nm\r\\F'Symbol's\\F'Arial'2 ="+num2str(varian2)






String name1= num2str(angle)+"DEWC"

Make $name1 = {q,B1,D1,R1,B2,D2,R2}

End

Function updateDoubleExpWCum(ctrl,ctrlVal,event): SliderControl

String ctrl



tempFit="tempFit"

Variable A1,B1,C1,A2,B2,C2



ControlInfo slideC1; C1=V_Value



ControlInfo slideC2; C2=V_Value



TitleBox valC1, title=num2str(C1)



TitleBox valC2, title=num2str(C2)

TitleBox valVarian1, title=num2str(C1/B1^2)

TitleBox valVarian2, title=num2str(C2/B2^2)




KillWaves tempFit

endif


Wave xs = $xVals

Wave fit = $tempFit

fit=(A1*exp(-B1*xs)*(1+C1*xs^2/2)+A2*exp(-B2*xs)*(1+C2*xs^2/2))^2

Rename fit, tempfit


End

// Functions for combining data from different angles for further data analysis

Function multipleAnglePlot()

NewPanel /W=(100,100,260,190) as "Mulit-Angle Plot"

TitleBox info1, pos={5,5}, title="Open files and fit all", frame=0

TitleBox info2, pos={5,30}, title="Press Start when ready", frame=0

Button start, pos={55,55}, size={60,20}, title="Start", proc=createPlot

End

Function createPlot(ctrl): ButtonControl

String ctrl

NVAR gT


setVars()

endif

String wave1,wave2,wave3,wave4,wave5

Variable number=5

Prompt wave1, "Angle1:", popup, WaveList("*",";","")

Prompt wave2, "Angle2:", popup, WaveList("*",";","")

Prompt wave3, "Angle3:", popup, WaveList("*",";","")+";_none_"



Variable type=0

DoPrompt "Select angles", wave1, wave2, wave3, wave4, wave5

if(cmpstr(wave5,"_none_")==0)

number=4

endif


number=3

endif


number=2

endif

Wave w1 = $wave1

Wave w2 = $wave2

if(number>2)

Wave w3 = $wave3

endif

if(number>3)

Wave w4 = $wave4

endif

if(number>4)

Wave w5 = $wave5

endif

if(numpnts(w1)>5)

type=1

endif

if(exists("qs"))

KillWaves qs,bs,q2

endif

Make /N=(number) qs, bs, q2

qs[0]=w1[0]

bs[0]=w1[1]

qs[1]=w2[0]

bs[1]=w2[1]

if(number>2)

qs[2]=w3[0]

bs[2]=w3[1]

endif

if(number>3)

qs[3]=w4[0]

bs[3]=w4[1]

endif

if(number>4)

qs[4]=w5[0]

bs[4]=w5[1]

endif

q2=qs^2

if(exists("qs2"))

KillWaves qs2,bs2,q22

endif

if(type==1)

Make/N=(number) qs2,bs2, q22

qs2[0]=w1[0]

bs2[0]=w1[4]

qs2[1]=w2[0]

bs2[1]=w2[4]

if(number>2)

qs2[2]=w3[0]

bs2[2]=w3[4]

endif

if(number>3)

qs2[3]=w4[0]

bs2[3]=w4[4]

endif

if(number>4)

qs2[4]=w5[0]

bs2[4]=w5[4]

endif

q22=qs2^2

endif

Display/K=1

AppendToGraph bs vs q2

if(type==1)

AppendToGraph bs2 vs q22

endif

if(exists("coefs"))

KillWaves coefs,fit_bs

endif

if(exists("coefs2"))

KillWaves coefs2,fit_bs2

endif

Make coefs={1}

if(exists("W_sigma"))

KillWaves W_sigma

endif

Make/N=1 W_sigma

NVAR gT

NVAR gETA

Variable D,R,sig,sigr

FuncFit/Q LineThroughZero kwCWave=coefs bs /X=q2 /D

sig=W_sigma[0]

D=coefs[0]

R=1.3806503*10^-23/6/Pi/D*gT/gETA

sigr=sig/D*R

NVAR gT

String texty="T= "+num2str(gT)+"\ry="+num2str(coefs[0])+"*x\rD= "+num2str(D)+" ± "+num2str(sig)+"

m\S2\M/s\rR\\Bh\\M ="+num2str(1000000000*R)+" ± "+num2str(1000000000*sigr)+" nm"

if(type==1)

Make coefs2={1}

Variable D2,R2,sig2,sigr2

FuncFit/Q LineThroughZero kwCWave=coefs2 bs2 /X=q22 /D

sig2=W_sigma[0]

D2=coefs2[0]

R2=1.3806503*10^-23/6/Pi/D2*gT/gETA

sigr2=sig2/D2*R2

String texty2="y2="+num2str(coefs2[0])+"*x\rD2= "+num2str(D2)+" ± "+num2str(sig2)+"

m\S2\M/s\rR\\Bh\\M2 ="+num2str(1000000000*R2)+" ± "+num2str(1000000000*sigr2)+" nm"

texty+="\r\r"

texty+=texty2

endif

TextBox/C/A=RB/N=text1/F=0 texty

Label left "\\Z14\\F'Symbol'G\\F'Arial'(s\\S-1\\M)"

Label bottom "\Z14q\S2\M\Z14(m\S-2\M\Z14)"

ModifyGraph mirror=2,fSize=12,axThick=1.5

ModifyGraph mode=3,mrkThick=1

ModifyGraph mrkThick=1.5

ModifyGraph mode(fit_bs)=0

if(type==1)

ModifyGraph mode(fit_bs2)=0

endif


Print sig,sig2

End

Rheology


// Rheology by AKS, 20130204

// This procedure works with data sets generated from a dynamic frequency temperature sweep test on an ARES

rheometer


Menu "Tools"

Submenu "Rheology"

"Load TTS, Shift, and Plot", TTSfull()

"Update Shifts", applyShifts()

"Plot Master Curve", plotMaster()

"Plot Shift Factors", plotShifts()

End

End

Function TTSfull()

loadTTS()

tempSep()

TTSShift()

plotMasterG1()

End

// Function to load the unshifted rheological data from a dynamic frequency temperature sweep test

Function loadTTS()

// Load the unshifted rheological data

String null="", name1

LoadWave/J/D/W/A/Q/K=0/L={0,27,0,0,5} /P=$null null

null=S_fileName

// Get new, more better file name

Prompt name1, "Select base name of "+null

DoPrompt "Enter Name", name1

//Make new names and rename loaded waves

String first=name1+"_FreqOrig", second=name1+"_G1Orig", third=name1+"_G2Orig",

fourth=name1+"_TanDOrig", fifth=name1+"_TempOrig"

Rename $StringFromList(0,S_waveNames), $first

Rename $StringFromList(1,S_waveNames), $second

Rename $StringFromList(2,S_waveNames), $third

Rename $StringFromList(3,S_waveNames), $fourth

Rename $StringFromList(4,S_waveNames), $fifth

String/G base=name1

End

// This function separates the data into isothermal frequency sweeps

Function tempSep()

SVAR base=base

String first=base+"_FreqOrig", second=base+"_G1Orig", third=base+"_G2Orig",

fourth=base+"_TanDOrig", fifth=base+"_TempOrig"

Wave freqs=$first

Wave G1s=$second

Wave G2s=$third

Wave TanDs=$fourth

Wave temps=$fifth

//Count how many freqs are in each scan

Variable freq1=freqs[0], i=1, numfreqs, j,k

do

if(freqs[i]==freq1)

numfreqs=i

break

endif

i+=1

while(1)

temps=round(temps)

i=0

do

j=0

String temp=base+"_"+num2str(temps[i]), curFreq=temp+"_Freq", curG1=temp+"_G1",

curG2=temp+"_G2", CurTD=temp+"_TanD", curTemp=temp+"_Temp"

String curFreq2=curFreq+"shifted", curG12=curG1+"shifted", curG22=curG2+"shifted",

CurTD2=curTD+"shifted", curTemp2=curTemp+"shifted"

Make/N=(numfreqs) $curFreq, $curG1, $curG2, $curTD, $curTemp, $curFreq2, $curG12,

$curG22, $curTD2, $curTemp2

Wave cfreq=$curFreq

Wave cfreq2=$curFreq2

Wave cg1=$curG1

Wave cg12=$curG12

Wave cg2=$curG2

Wave cg22=$curG22

Wave ctd=$curTD

Wave ctd2=$curTD2

Wave ctemp=$curTemp

Wave ctemp2=$curTemp2

do

cfreq[j]=freqs[i+j]

cg1[j]=G1s[i+j]

cg2[j]=G2s[i+j]

ctd[j]=TanDs[i+j]

ctemp[j]=temps[i+j]

cfreq2[j]=freqs[i+j]

cg12[j]=G1s[i+j]

cg22[j]=G2s[i+j]

ctd2[j]=TanDs[i+j]

ctemp2[j]=temps[i+j]

j+=1

while(j<numfreqs)

i+=numfreqs

while(i<numpnts(temps))

End

// This function loads the shift factors and shifts the data using applyShifts()

Function TTSshift()

SVAR base=base

String null="", curtemp

LoadWave/J/D/W/A/Q/K=0/L={0,19,0,0,3} /P=$null null

String first=base+"_Temps", second=base+"_As", third=base+"_Bs"

Rename $StringFromList(0,S_waveNames), $first

Rename $StringFromList(1,S_waveNames), $second

Rename $StringFromList(2,S_waveNames), $third

Wave temps=$first

Wave as=$second

Wave bs=$third

temps=round(temps)

Edit/K=1 $first, $second, $third

applyShifts()

End

// This functino shifts the data using the leaded shift factors

Function applyShifts()

SVAR base=base

String first=base+"_Temps", second=base+"_As", third=base+"_Bs",curtemp

Wave temps=$first

Wave as=$second

Wave bs=$third

Variable i=0

do

curtemp=num2str(temps[i])

Wave cfr=$(base+"_"+curtemp+"_Freq")

Wave cg1=$(base+"_"+curtemp+"_G1")

Wave cg2=$(base+"_"+curtemp+"_G2")

Wave cfr2=$(base+"_"+curtemp+"_Freqshifted")

Wave cg12=$(base+"_"+curtemp+"_G1shifted")

Wave cg22=$(base+"_"+curtemp+"_G2shifted")

cfr2=as[i]*cfr

cg12=bs[i]*cg1

cg22=bs[i]*cg2

i+=1

while(i<numpnts(temps))

End

// This function plots the storage modulus of the master curve (full shifted data set)

Function plotMasterG1()

SVAR base=base

String xs=WaveList("*Freqshifted",";","")

String ys=WaveList("*G1shifted",";","")

Display/K=1

Variable i=0

do

String x=StringFromList(i,xs), y=StringFromList(i,ys)

if(strlen(x)==0)

break

endif

AppendToGraph $y vs $x

i+=1

while(1)

ModifyGraph mode=2,lsize=2

ModifyGraph log=1,tick=2,mirror=1,fStyle=1,fSize=12,axThick=1.5;DelayUpdate

ModifyGraph lblMargin(left)=10,standoff=0;DelayUpdate

Label left "\\Z12\\f01Storgae Modulus (Pa)";DelayUpdate

Label bottom "\\Z12\\f01Shifted Frequency (Hz)"

End

// This function plots the loss modulus of the master curve (full shifted data set)

Function plotMasterG2()

SVAR base=base


String ys=WaveList("*G2shifted",";","")

Display/K=1

Variable i=0

do

String x=StringFromList(i,xs), y=StringFromList(i,ys)

if(strlen(x)==0)

break

endif

AppendToGraph $y vs $x

i+=1

while(1)


ModifyGraph rgb=(0,0,65280)



Label left "\\Z12\\f01Loss Modulus (Pa)";DelayUpdate


End

// This function plots the storage and loss moduli of the master curve (full shifted data set)

Function plotMasterBoth()

SVAR base=base


String ys1=WaveList("*G1shifted",";","")

String ys2=WaveList("*G2shifted",";","")

Display/K=1

Variable i=0

do

String x=StringFromList(i,xs), y1=StringFromList(i,ys1), y2=StringFromList(i,ys2)

if(strlen(x)==0)

break

endif

AppendToGraph $y1 vs $x

AppendToGraph $y2 vs $x

ModifyGraph rgb($y2)=(0,0,65280)

i+=1

while(1)




Label left "\\Z12\\f01Modulus (Pa)";DelayUpdate


End

// This function plots the master curve (full shifted data) in any form

Function plotMaster()

String choice=""

Prompt choice, "What to Plot", popup, "Storage Modulus;Loss Modulus;Storage and Loss"

DoPrompt "Plot Options", choice

if(stringmatch(choice,"Storage Modulus"))

plotMasterG1()

endif

if(stringmatch(choice,"Loss Modulus"))

plotMasterG2()

endif

if(stringmatch(choice,"Storage and Loss"))

plotMasterBoth()

endif

End

// This function plots the shift factors in the typical manner

Function plotShifts()

SVAR base=base

String t=base+"_Temps", a=base+"_As", b=base+"_Bs"

Display/K=1 $a vs $t

AppendToGraph/R/C=(0,0,65280) $b vs $t

ModifyGraph log(left)=1,tick=2,mirror(bottom)=2,fStyle=1,fSize=12,axThick=1.5;DelayUpdate

ModifyGraph standoff=0;DelayUpdate

Label left "\\Z12\\f01Horizontal Shift";DelayUpdate

Label bottom "\\Z12\\f01Temperature";DelayUpdate

Label right "\\Z12\\f01Vertical Shift";DelayUpdate

SetAxis right 0,1

ModifyGraph lsize=2

End

Sec5Tools


// Sec5Tools by AKS, 20130204

// This procedure works with data sets generated at 5-ID-D at the Advanced Photon Source at Argonne National

Labs


Menu "Tools"

Submenu "SAXS"

Submenu "Sector 5"

"Sector 5 Tools", APSTools()

End

"-",

End

End

Function/S GetLeafName(pathStr)

String pathStr

String leafName

Variable pos

leafName = ""

pos = strlen(pathStr) - 1 // Search from the

end

do

if (CmpStr(pathStr[pos], ":") == 0) // Found the colon?

leafName = pathStr[pos+1, strlen(pathStr)]

break

// Break out of loop.

endif

pos -= 1

while(pos > 0)

return leafName

End

Function APSLoadDir(pathName)

String pathName

String fileName

Variable index=0



if (V_flag != 0)


endif


endif


fileName = IndexedFile($pathName, index, ".txt")


break // Break

out of loop

endif

// Load files section

// This section extracts the user initials, data type, and frames (exposures) from the file name

String expr="([[:alpha:]]+)[_]([[:alpha:]]+)[_]([[:digit:]]+)[_]([[:digit:]]+)([[:alpha:]]+)([[:digit:]]+)"

String inits, type, scan, frame1, to, frame2

SplitString/E=expr (fileName), inits, type, scan, frame1, to, frame2

if(V_flag==6)

if(stringmatch(type,"saxs")==1)

APSLoad(pathName,fileName)

endif

endif

if(V_flag==0)

expr="([[:alpha:]]+)[_]([[:alpha:]]+)[_]([[:digit:]]+)[_]"

SplitString/E=expr (fileName), inits, type, scan

Wave scans=root:APS:Info:ScanNo

Wave frames=root:APS:Info:Frames

Variable scan2=str2num(scan)

Variable i=0

Variable frame

do

if(scans[i]==scan2)

frame=frames[i]

break

endif

i=i+1

while(i<numpnts(scans))

if(frame==1)

if(stringmatch(type,"saxs")==1)

APSLoad(pathName, fileName)

endif

endif

endif

//End load files section

index += 1

while (1)

if (Exists("temporaryPath")) // Kill temp path if it exists


endif


End

Function APSLoad(pathName, fileName)

String pathName // Name of an existing IGOR symbolic path or ""

String fileName // Name of file within folder pointed to by symbolic path or ""

SetDataFolder root:APS

// If either of the input parameters is "", put up a dialog to get file.

if ((strlen(pathName)==0) %| (strlen(pathName)==0))

Variable dummyRefNum

String pathToFolder

Open/R/D/M="Choose data file" dummyRefNum // This sets an automatically created

local variable named S_fileName.

if (strlen(S_fileName) == 0) // User cancelled?

return -1

endif

// Now break the full path to file down into path to folder plus file name.

// This is done by searching for the last colon in the full path.

fileName =GetLeafName(S_fileName)

if (strlen(fileName) == 0)

Print "LoadDataSetFromFile bug"

return -1

endif

pathToFolder = S_fileName[0, strlen(S_fileName) - strlen(fileName) - 1]

// Make sure there is an IGOR symbolic path pointing to the folder

NewPath/O/Q CurrentDataFilePath pathToFolder

pathName = "CurrentDataFilePath"

endif

//Find beginning of data

LoadWave/J/D/K=0/L={0,0,0,0,1}/B="N=finder;"/P=$pathName/W/A fileName

String finder="finder"

Wave/T find=finder

Variable i=0

Variable datastart=-1

do

if(strsearch(find[i],"#",0)==-1)

datastart=i

break

endif

i=i+1

while(i<numpnts(find))

KillWaves find

//Print datastart Prints starting line of data, end of header

String expr="([[:alpha:]]+)[_]([[:alpha:]]+)[_]([[:digit:]]+)[_]"

String inits, type, scan

SplitString/E=expr (fileName), inits, type, scan


Wave/T sams=root:APS:Info:Sample

Wave temps=root:APS:Info:Temp


i=0

String sample

Variable temp

do

if(scans[i]==scan2)

temp=temps[i]

sample=sams[i]

break

endif

i=i+1

while(i<numpnts(scans))

NewDataFolder/O/S $sample

String tempst=num2str(temp)+"C"+scan

String

columninfo="N='_skip_';N=q"+tempst+";N=i"+tempst+";N=ie"+tempst+";C=2,N='_skip_';N=iqs"+tempst+";C=15,

N='_skip_';"

LoadWave/A/B=columninfo/D/J/K=0/L={datastart,datastart+1,0,0,0}/P=$pathName/W fileName

End

//Load info file to parse scan number info from (sample name, temperature, frames)

Function getInfoFile(pathName, fileName)

String pathName, fileName

SetDataFolder root:APS




String pathToFolder




return -1

endif



fileName = GetLeafName(S_fileName)



return -1

endif





endif

NewDataFolder/O/S Info

LoadWave/J/D/W/A/K=0/B="F=0,N=ScanNo; F=-2,N=Sample; F=0,N=Temp; F=0,N=Frames;"

/P=$pathName fileName

End

// Retrieve data folders and waves from folders

Function/S getObjects(path, objectType)

String path

Variable objectType

DFREF pathref=$path

String list="", name

Variable i=0

do

name=GetIndexedObjNameDFR(pathref,objectType,i)

if(strlen(name)==0)

list=list[0,strlen(list)-2]

break

endif

if(stringmatch(name,"info")==0)

list+=name+";"

endif

i+=1

while(1)

return list

End

// Function to get a list of all APS generated waves that can be plotted

Function/S getAllWavesAPS()

String mainList="",subList="",item="", sub="", result=""

mainList=getObjects("root:APS:",4)

Variable i=0

do

item=StringFromList(i,mainList)

if(strlen(item)==0)

result=result[0,strlen(result)-2]

break

endif

DFREF path=root:APS:$item

SetDataFolder path

subList=getObjects(":",1)

Variable j=0

do

sub=StringFromList(j,subList)

if(strlen(sub)==0)

break

endif

if(stringmatch(sub[0],"q")==1)

String expr="[q]([[:digit:]]+)[C]([[:digit:]]+)"

String temp,scan

SplitString/E=expr (sub), temp, scan

result+=item+" - "+temp+"C - Scan "+scan+";"

endif

j+=1

while(1)

i+=1

while(1)

SetDataFolder root:

return result

End

Function test()

Print getAllWavesAPS()

End

// Function to get all other waves that have been imported

Function/S getAllWavesLS()

String mainList="",subList="",item="", sub="", result=""

mainList=getObjects("root:LS:",4)

Variable i=0

do

item=StringFromList(i,mainList)

if(strlen(item)==0)

result=result[0,strlen(result)-2]

break

endif

DFREF path=root:LS:$item

SetDataFolder path

subList=getObjects(":",1)

Variable j=0

do

sub=StringFromList(j,subList)

if(strlen(sub)==0)

break

endif

if(stringmatch(sub[0],"q")==1)

String expr="[q]([[:digit:]]+)[C]([[:digit:]]+)"

String temp,scan

SplitString/E=expr (sub), temp, scan

result+=item+" - "+temp+"C - Scan "+scan+";"

endif

j+=1

while(1)

i+=1

while(1)

SetDataFolder root:

return result

End

// Function to retireve all plottable waves

Function/S getAllWaves()

String waveaps=getAllWavesAPS(), wavels=getAllWavesLS(), result=""

if(strlen(waveaps)==0)

return wavels

endif

if(strlen(wavels)==0)

return waveaps

endif

return waveaps+";"+wavels

End

// Function that translates strings

Function/S getStuffFromString(str)

String str

Variable pt1, pt2

pt1=strsearch(str," - ",0)

pt2=strsearch(str,"C - Scan",0)

String folder, temp, scan, result

folder=str[0,pt1-1]

temp=str[pt1+3,pt2-1]

scan=str[pt2+9,strlen(str)-1]

result=folder+";q"+temp+"C"+scan

return result

End

Function checkaction(ctrlName,checked):CheckBoxControl

String ctrlName

Variable checked

if(stringmatch(ctrlName,"new")==1)

if(checked==1)

Checkbox app, value=0

Checkbox rem, value=0

Button go, title="Plot New!"

endif

endif

if(stringmatch(ctrlName,"app")==1)

if(checked==1)

Checkbox new, value=0


Button go, title="Append!"

endif

endif

if(stringmatch(ctrlName,"rem")==1)

if(checked==1)



Button go, title="Remove!"

endif

endif

if(stringmatch(ctrlName,"over")==1)

if(checked==1)

Checkbox stac, value=0

endif

endif

if(stringmatch(ctrlName,"stac")==1)

if(checked==1)

Checkbox over, value=0

endif

endif

if(stringmatch(ctrlName,"ivq")==1)

if(checked==1)

Checkbox iq2vq, value=0

endif

endif

if(stringmatch(ctrlName,"iq2vq")==1)

if(checked==1)

Checkbox ivq, value=0

endif

endif

End

Function butaction(ctrlName):ButtonControl

String ctrlName

if(stringmatch(ctrlName,"go")==1)

String wavepickval,waveinf

Variable newval, appval, remval, overval, stacval, ivqval, iq2vqval

ControlInfo wavepick; wavepickval=S_Value

ControlInfo new;newval=V_Value

ControlInfo app;appval=V_Value

ControlInfo rem;remval=V_Value

ControlInfo over;overval=V_Value

ControlInfo stac;stacval=V_Value

ControlInfo ivq;ivqval=V_Value

ControlInfo iq2vq;iq2vqval=V_Value

waveinf=getStuffFromString(wavepickval)

String y,x,curwave, fold=stringfromlist(0,waveinf), leg=""

DFREF path=root:APS:$fold

x=stringfromlist(1,waveinf)

if(ivqval==1)

y="i"+x[1,strlen(x)-1]

else

y="iqs"+x[1,strlen(x)-1]

endif

if(newval==1)

Display/K=1 path:$y vs path:$x

ModifyGraph log(left)=1,lsize=1.5,mirror=2,fSize=12,axThick=1.5;DelayUpdate

Label left "\\Z14I (a.u.)";DelayUpdate

Label bottom "\\Z14q (Å\\S-1\\M\\Z14)"

endif

if(appval==1)

if(strlen(StringfromList(0,WinList("*",";","WIN:1")))==0)

Display/K=1 path:$y vs path:$x

ModifyGraph log(left)=1,lsize=1.5,mirror=2,fSize=12,axThick=1.5;DelayUpdate



else

Appendtograph path:$y vs path:$x

ModifyGraph

log(left)=1,lsize=1.5,mirror=2,fSize=12,axThick=1.5;DelayUpdate



if(stacval==1)

Variable num=1,j=0

do

curwave=WaveName("",j,1)

if(strlen(curwave)==0)

break

endif

j+=1

num=10*num

while(1)

ModifyGraph muloffset($y)={0,num}

endif

endif

endif

if(remval==1)

Variable i=0

do

curwave=WaveName("",i,1)


break

endif

if(stringmatch(y,curwave)==1)

RemoveFromGraph $y

endif

i+=1

while(1)

endif

i=0

do



break

endif

ModifyGraph rgb($curwave)=(getR(i),getG(i),getB(i))

i+=1

String expr="([[:digit:]]+)[C]([[:digit:]]+)"

String temp,scan

SplitString/E=expr (curwave), temp, scan


Wave/T sams=root:APS:Info:Sample


j=0

String sample

do

if(scans[j]==scan2)

sample=sams[j]

break

endif

j=j+1

while(j<numpnts(scans))

leg+="\\s(\'"+curwave+"\')"+sample+" - "+temp+"C - Scan "+scan+"\r"

while(1)

leg=leg[0,strlen(leg)-2]

Legend/C/N=text0/A=RT leg

endif

if(stringmatch(ctrlname,"addlines")==1)

APSAddLines()

endif

if(stringmatch(ctrlname,"loadinfo")==1)

getInfoFile("","")

endif

if(stringmatch(ctrlname,"loadonefile")==1)

APSLoad("","")

PopupMenu wavepick, value=getAllWaves()

PopupMenu backpick, value=getAllWaves()

endif

if(stringmatch(ctrlname,"loaddirect")==1)

APSLoadDir("")

PopupMenu wavepick, value=getAllWaves()

PopupMenu backpick, value=getAllWaves()

endif

if(stringmatch(ctrlname,"subtract")==1)

APSSubtract()

endif

End

Function getR(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 1:

case 8:

result=65280

break

case 3:

case 4:

case 5:

case 6:

result=0

break

case 7:

result=39440

break

case 2:

result=52224

break

endswitch

return result

End

Function getG(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 6:

case 7:

case 8:

result=0

break

case 1:

case 5:

result=43520

break

case 3:

case 4:

result=65280

break

case 2:

result=52224

break

endswitch

return result

End

Function getB(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 1:

case 2:

case 3:

result=0

break

case 4:

case 5:

case 6:

result=65280

break

case 7:

result=58880

break

case 8:

result=52224

break

endswitch

return result

End

Function APSAddLines()

NewDataFolder/O/S root:APS:temp

String winf, winf2, wpath, type, ywave

String/G xwave

ControlInfo wavepick; winf=S_Value

winf2=getStuffFromString(winf)

wpath=StringFromList(0,winf2)

xwave=StringFromList(1,winf2)

Variable val

ControlInfo ivq; val=V_Value

if(val==1)

ywave="i"+xwave[1,strlen(xwave)-1]

else

ywave="iqs"+xwave[1,strlen(xwave)-1]

endif

DFREF path=root:APS:$wpath

Wave xs=path:$xwave

Wave ys=path:$ywave

String x2="x2"+xwave, y2="y2"+xwave, leg="\\s(\'"+y2+"\') "+winf

SetDataFolder root:APS:temp

Duplicate xs, $x2

Duplicate ys, $y2

Display/K=1/N=difflinesplot $y2 vs $x2

WAVE x2w=$x2

WAVE y2w=$y2

ModifyGraph log(left)=1,lsize=1.5,mirror=2,fSize=12,axThick=1.5;


Variable maxx=WaveMax(y2w),maxy

Variable i=0

do

if(y2w[i]==maxx)

maxy=x2w[i]

break

endif

i+=1

while(i<numpnts(y2w))

Variable L,C,S,G,start //range, beam

NewPanel /K=2/W=(100,100,400,420) as "Add Diffraction Lines"

TitleBox titleL, pos={5,5}, title="L=", frame=0

TitleBox titleC, pos={5,85}, title="C=", frame=0, fColor=(0,0,65535)

TitleBox titleS, pos={5,165}, title="S=", frame=0, fColor=(0,30000,0)

TitleBox titleG, pos={5,245}, title="G=", frame=0, fColor=(65535,0,0)

Slider slideL, limits={.0001,.1,0}, value=maxy, pos={5,20}, size={200,50}, vert=0, ticks=1, variable=L,

proc=APSupdateSlider

Slider slideC, limits={.0001,.1,0}, value=maxy, pos={5,100}, size={200,50}, vert=0, ticks=1, variable=C,

proc=APSupdateSlider, fColor=(0,0,65535)

Slider slideS, limits={.0001,.1,0}, value=maxy, pos={5,180}, size={200,50}, vert=0, ticks=1, variable=S,


Slider slideG, limits={.0001,.1,0}, value=maxy, pos={5,260}, size={200,50}, vert=0, ticks=1, variable=G,


TitleBox valL, pos={20,5}, title=num2str(L), frame=0

TitleBox valC, pos={20,85}, title=num2str(C), frame=0, fColor=(0,0,65535)

TitleBox valS, pos={20,165}, title=num2str(S), frame=0, fColor=(0,30000,0)

TitleBox valG, pos={20,245}, title=num2str(g), frame=0, fColor=(65535,0,0)

TitleBox titleL1, pos={240,20}, title="Lamellae", frame=0

TitleBox titleC1, pos={240,100}, title="Cylinders", frame=0, fColor=(0,0,65535)

TitleBox titleS1, pos={240,180}, title="Spheres", frame=0, fColor=(0,30000,0)

TitleBox titleG1, pos={240,260}, title="Gyroid", frame=0, fColor=(65535,0,0)

Checkbox checkL, value=0, pos={220,20}, title="", proc=APSupdateCheck

Checkbox checkC, value=0, pos={220,100}, title="", proc=APSupdateCheck

Checkbox checkS, value=0, pos={220,180}, title="", proc=APSupdateCheck

Checkbox checkG, value=0, pos={220,260}, title="", proc=APSupdateCheck

Button closer, pos={220,290}, title="Close", proc=APSclose

APSupdateLines()

End

Function APSclose(ctrlName):ButtonControl

String ctrlName


KillVariables/A

String lamw,lamx,lamy,lamw2

lamw="lamw"

lamx="lamx"

lamy="lamy"

lamw2="lamw2"

if(exists("lamy")) //Remove from graph if unchecked and get rid of old waves

RemoveFromGraph/W=difflinesplot $lamy

KillWaves/Z $lamy,$lamx,lw,lw2

endif

String cylw,cylx,cyly,cylw2

cylw="cylw"

cylx="cylx"

cyly="cyly"

cylw2="cylw2"

if(exists("cyly")) //Remove from graph if unchecked and get rid of old waves

RemoveFromGraph/W=difflinesplot $cyly

KillWaves/Z $cyly,$cylx,cw,cw2

endif

String sphw,sphx,sphy,sphw2

sphw="sphw"

sphx="sphx"

sphy="sphy"

sphw2="sphw2"

if(exists("sphy")) //Remove from graph if unchecked and get rid of old waves

RemoveFromGraph/W=difflinesplot $sphy

KillWaves/Z $sphy,$sphx,sw,sw2

endif

String gyrw,gyrx,gyry,gyrw2

gyrw="gyrw"

gyrx="gyrx"

gyry="gyry"

gyrw2="gyrw2"

if(exists("gyry")) //Remove from graph if unchecked and get rid of old waves

RemoveFromGraph/W=difflinesplot $gyry

KillWaves/Z $gyry,$gyrx,gw,gw2

endif

String name="difflinesplot"

DoWindow/K $WinName(0,64)

DoWindow/C olddifflinesplot

End

Function APSupdateSlider(ctrl,ctrlVal,event): SliderControl

String ctrl


APSupdateLines()

End

Function APSupdateCheck(ctrl,val): CheckboxControl

String ctrl

Variable val

APSupdateLines()

End

Function APSupdateLines()


SVAR xwave=xwave

String x2="x2"+xwave,y2="y2"+xwave

Wave ys =root:APS:temp:$y2

Wave xs = root:APS:temp:$x2

Variable max1=WaveMax(xs)

Variable L,C,S,G,lon,con,son,gon,i,j //range, beam, bon

ControlInfo slideL; L=V_Value


ControlInfo slideS; S=V_Value

ControlInfo slideG; G=V_Value

ControlInfo checkL; lon=V_Value

ControlInfo checkC; con=V_Value

ControlInfo checkS; son=V_Value

ControlInfo checkG; gon=V_Value

Slider slideL, limits={.0001,0.1,0}

Slider slideC, limits={.0001,0.1,0}

Slider slideS, limits={.0001,0.1,0}

Slider slideG, limits={.0001,0.1,0}

TitleBox valL, title=num2str(L)


TitleBox valS, title=num2str(S)

TitleBox valG, title=num2str(G)


lamw="lamw"

lamx="lamx"

lamy="lamy"

lamw2="lamw2"




endif


cylw="cylw"

cylx="cylx"

cyly="cyly"

cylw2="cylw2"




endif


sphw="sphw"

sphx="sphx"

sphy="sphy"

sphw2="sphw2"




endif


gyrw="gyrw"

gyrx="gyrx"

gyry="gyry"

gyrw2="gyrw2"




endif

if(lon>0) //Add lam diffraction lines if checked

Make lw={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20}

i=0

j=20

do

if(L*lw[i]>max1)

j=i

break

endif

i+=1

while(i<numpnts(lw))

i=0

Make/N=(j) lw2

do

lw2[i]=lw[i]

i+=1

while(i<j)

Duplicate lw2,$lamx,$lamy

Wave lx = $lamx

Wave ly = $lamy

lx=L*lw2

i=0

j=0

do

do

if(xs[j]>lx[i])

ly[i]=ys[j]

break

endif

j+=1

while(j<numpnts(xs))

i+=1

while(i<numpnts(lx))

rename ly, $lamy

rename lx, $lamx

appendToGraph/W=difflinesplot ly vs lx

ModifyGraph/W=difflinesplot mode(lamy)=1,rgb(lamy)=(0,0,0)

endif

if(con>0) //Add cyl diffraction lines if checked

Make cw={1,3,4,7,9,12,13,16,19,21,25,27,28,31,36,37,39,43,48,49,52,57,61,63,64,67,73,75,76,79}

i=0

j=30

do

if(C*cw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(cw))

i=0

Make/N=(j) cw2

do

cw2[i]=cw[i]^(1/2)

i+=1

while(i<j)

Duplicate cw2,$cylx,$cyly

Wave cx = $cylx

Wave cy = $cyly

cx=C*cw2

i=0

j=0

do

do

if(xs[j]>cx[i])

cy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(cx))

rename cy, $cyly

rename cx, $cylx

appendToGraph/W=difflinesplot cy vs cx

ModifyGraph/W=difflinesplot mode(cyly)=1,rgb(cyly)=(0,0,65535)

endif

if(son>0) //Add sph diffraction lines if checked

Make

sw={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,

40}

i=0

j=40

do

if(S*sw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(sw))

i=0

Make/N=(j) sw2

do

sw2[i]=sw[i]^(1/2)

i+=1

while(i<j)

Duplicate sw2,$sphx,$sphy

Wave sx = $sphx

Wave sy = $sphy

sx=S*sw2

i=0

j=0

do

do

if(xs[j]>sx[i])

sy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(sx))

rename sy, $sphy

rename sx, $sphx

appendToGraph/W=difflinesplot sy vs sx

ModifyGraph/W=difflinesplot mode(sphy)=1,rgb(sphy)=(0,30000,0)

endif

if(gon>0) //Add gyr diffraction lines if checked

Make gw={6,8,14,16,20,22,24,26,30,32,38,40,42,46,48,50,52,54,56,62}

i=0

j=20

do

if(G*gw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(gw))

i=0

Make/N=(j) gw2

do

gw2[i]=gw[i]^(1/2)

i+=1

while(i<j)

Duplicate gw2,$gyrx,$gyry

Wave gx = $gyrx

Wave gy = $gyry

gx=G*gw2

i=0

j=0

do

do

if(xs[j]>gx[i])

gy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(gx))

rename gy, $gyry

rename gx, $gyrx

appendToGraph/W=difflinesplot gy vs gx

ModifyGraph/W=difflinesplot mode(gyry)=1,rgb(gyry)=(65535,0,0)

endif

End

Function APSSubtract()

String wave1val, backval, wave1, back, wave1root, backroot, wave1q, backq

ControlInfo wavepick; wave1val=S_Value

ControlInfo backpick; backval=S_Value

wave1root=StringfromList(0,getStuffFromString(wave1val))

wave1q=StringfromList(1,getStuffFromString(wave1val))

backroot=StringfromList(0,getStuffFromString(backval))

backq=StringfromList(1,getStuffFromString(backval))

wave1="i"+wave1q[1,strlen(wave1q)-1]

back="i"+backq[1,strlen(backq)-1]

DFREF wpath=root:APS:$wave1root

DFREF bpath=root:APS:$backroot

Wave q1=wpath:$wave1q

Wave w1=wpath:$wave1

Wave b1=bpath:$back

Display/K=1/L=topleft/B=bottom1 w1 vs wpath:$wave1q

AppendToGraph/L=topleft/B=bottom1 b1 vs bpath:$backq

SetDataFolder root:APS:$wave1root

NewDataFolder/O/S BackCorr

String neww="bc"+wave1

String newx="bc"+wave1q

Duplicate w1, $neww

Duplicate q1, $newx

Wave w2=$neww

w2=w1-b1

AppendToGraph/L=bottomleft/B=bottom2 w2 vs wpath:$wave1q

ModifyGraph log(topleft)=1, log(bottomleft)=1, lsize=1.5, axisEnab(topleft)={0.5,1},

axisEnab(bottomleft)={0,0.5}, freePos(topleft)=0, freePos(bottomleft)=0

ModifyGraph rgb($neww)=(0,0,65535), rgb($back)=(0,0,0), freePos(bottom1)=0,

freePos(bottom2)={0.5,kwFraction}

End

Function subt(ctrlName):ButtonControl

String ctrlName

Variable highy, highb, highdiff, lowdiff

Wave y1=CsrWaveRef(A)

Wave x1=CsrXWaveRef(A)

Wave by=CsrWaveRef(B)

Wave bx=CsrXWaveRef(B)

highy=getAveYFromEnd(y1,numpnts(y1)-xcsr(B))

highb=getAveYFromEnd(by,numpnts(by)-xcsr(B))

Print highy, highb

End

Function getAveYFromEnd(w1,numpts)

Wave w1

Variable numpts

Variable i=numpnts(w1)-numpts, total=0, num=0

do

total+=w1[i]

num+=1

i+=1

while(i<numpnts(w1))

return total/num

End

Function APSTools()

SetDataFolder root:

NewDataFolder/O LS

NewDataFolder/O/S APS

NewPanel /k=1/N=APSToolKit/W=(10,10,210,435)

//Section for loading data

TitleBox title0, title="Load Data Files", pos={5,5}, frame=0

Button loadinfo, pos={5,20}, title="Load Info File", proc=butaction, size={80,20}

Button loadonefile, pos={5,40}, title="Load One File", proc=butaction, size={80,20}

Button loaddirect, pos={5,60}, title="Load Directory of Files", proc=butaction, size={120,20}

//Section for plotting data

TitleBox title1, title="Select Wave to Plot", pos={5,90}, frame=0

PopupMenu wavepick, value=getAllWaves(), noproc, pos={5,105}

TitleBox title2, title="Select Operation", pos={5,135}, frame=0

CheckBox new, mode=1, pos={5,150}, value=1,title="Create New Graph", proc=checkaction

CheckBox app, mode=1, pos={5,165},value=0, title="Append to Top Graph", proc=checkaction

CheckBox rem, mode=1, pos={5,180},value=0, title="Remove from Top Graph", proc=checkaction

TitleBox title3, title="Select Plot Style", pos={5,200}, frame=0

CheckBox over, mode=1,pos={5,215},value=1, title="Overlay Plot", proc=checkaction

CheckBox stac, mode=1, pos={5,230},value=0, title="Stacked Plot", proc=checkaction

TitleBox title4, title="Select Plot Type", pos={5,250}, frame=0

CheckBox ivq, mode=1,pos={5,265},value=1, title="Plot I vs. q", proc=checkaction

CheckBox iq2vq, mode=1,pos={5,280},value=0, title="Plot I*q^2 vs. q", proc=checkaction

Button go, pos={5,300}, title="Plot!", proc=butaction, size={80,20}

//Section for adding diffraction lines - brings up external panel

Button addlines, pos={5,330}, title="Add Diffraction Lines", proc=butaction, size={120,20}

//Section for background subtraction

TitleBox title5, title="Select Background Wave", pos={5,360}, frame=0

PopupMenu backpick, value=getAllWaves(), noproc, pos={5,375}

Button subtract, pos={3,400}, title="Subtract", proc=butaction, size={80,20}

End

Sec12Tools


// Sec12Tools by AKS, 20130204

// This procedure works with .dat files generated at 12-ID-B at the Advanced Photon Source at Argonne National

Labs


Menu "Tools"

Submenu "SAXS"

Submenu "Sector 12"

"Sector 12 Tools", sector12tools()

"Lines", sec12lines()

End

"-"

End

End

Function/S GetLeafName12(pathStr)

String pathStr

String leafName

Variable pos

leafName = ""

pos = strlen(pathStr) - 1 // Search from the

end

do

if (CmpStr(pathStr[pos], ":") == 0) // Found the colon?

leafName = pathStr[pos+1, strlen(pathStr)]

break

// Break out of loop.

endif

pos -= 1

while(pos > 0)

return leafName

End

// Function to load an entire directory of files

Function Sec12LoadDir(pathName)

String pathName

String fileName

Variable index=0



if (V_flag != 0)


endif


endif


fileName = IndexedFile($pathName, index, ".dat")


break // Break

out of loop

endif

//Load files section

Sec12LoadOne(pathName,fileName)

//End load files section

index += 1

while (1)

// Kill temp path if it exists

if (Exists("temporaryPath"))


endif

// Signifies success.

return 0

End

// Function to load one file

Function Sec12LoadOne(pathName, fileName)

String pathName // Name of an existing IGOR symbolic path or ""

String fileName // Name of file within folder pointed to by symbolic path or ""

NewDataFolder/O/S root:Sec12




String pathToFolder




return -1

endif



fileName =GetLeafName12(S_fileName)



return -1

endif





endif

//Load sector 12 data

//String expr="([[:alnum:]]+)[_]([[:digit:]]+)[_]([[:digit:]]+)"

String name, scan, frame

//SplitString/E=expr (fileName), name, scan, frame

name=filename[0,strlen(filename)-13], scan=filename[strlen(filename)-11,strlen(filename)-9]

String type=name[0], name2=name[1,strlen(name)]+"_"+scan

//Next line gives column info, eg how to name different waves and which ones to throw away

String

columninfo="N="+type+"q"+name2+";N="+type+"i"+name2+";N="+type+"e"+name2+";N='_skip_';N='_skip_';N=

'_skip_';"

LoadWave/A/B=columninfo/D/J/K=0/V={"\t, "," $",0,0}/P=$pathName/W fileName

End

// Function to retrieve list of loaded waves

Function/S Sec12getwaves()


//get waves that start with Si

String list = Wavelist("Si*",";",""), cur, list2=""

//Remove the Si to get more human readable wave names

Variable index=0

do

cur=stringfromlist(index,list)

if(stringmatch(cur,"")==1)

break

endif

list2+=cur[2,strlen(cur)]+";"

index+=1

while(1)

//Remove the last semicolon

list2=list2[0,strlen(list2)-2]

return list2

End

// Function to combine SAXS and WAXS data for get SWAXS data

Function sec12combine()

String list=Sec12getWaves(),cur

Variable index=0, i=0

do

cur=stringfromlist(index,list)

if(stringmatch(cur,"")==1)

break

endif

//Combine the q waves

String wavesq="Sq"+cur, wavewq="Wq"+cur, waveswq="SWq"+cur

Wave wsq = $wavesq

Wave wwq = $wavewq

Make/N=(numpnts(wsq)+numpnts(wwq)) $waveswq

Wave wswq = $waveswq

wswq=wswq+wsq

i=0

do

wswq[numpnts(wsq)+i]=wwq[i]

i+=1

while(i<numpnts(wwq))

//Combine the i waves

String wavesi="Si"+cur, wavewi="Wi"+cur, waveswi="SWi"+cur

Wave wsi = $wavesi

Wave wwi = $wavewi

Make/N=(numpnts(wsi)+numpnts(wwi)) $waveswi

Wave wswi = $waveswi

wswi=wswi+wsi

i=0

do

wswi[numpnts(wsi)+i]=wwi[i]

i+=1

while(i<numpnts(wwi))

//Combine the e waves

String wavese="Se"+cur, wavewe="We"+cur, waveswe="SWe"+cur

Wave wse = $wavese

Wave wwe = $wavewe

Make/N=(numpnts(wse)+numpnts(wwe)) $waveswe

Wave wswe = $waveswe

wswe=wswe+wse

i=0

do

wswe[numpnts(wse)+i]=wwe[i]

i+=1

while(i<numpnts(wwe))

//Now loop through all waves

index+=1

while(1)

End

Function Sector12Tools()

NewPanel/k=1/N=Sector12Tools/W=(10,10,200,390)

// Data Loading section

TitleBox title0, title="Load Files", pos={5,5}, frame=0

TitleBox ver, title="AKS v1.1", pos={140,5}, frame=0

Button loadone, pos={5,20}, title="Load One File", proc=sec12but, size={80,20}

Button loaddir, pos={5,40}, title="Load Directory", proc=sec12but, size={80,20}

Button combine, pos={5,60}, title="Combine Data", proc=sec12but, size={80,20}

// Data plotting section

TitleBox title1, title="Select Wave to Plot", pos={5,90}, frame=0

PopupMenu wavepick, value=Sec12getWaves(), noproc, pos={5,105}

TitleBox title2, title="Select Operation", pos={5,135}, frame=0

CheckBox new, mode=1, pos={5,150}, value=1,title="Create New Graph", proc=sec12check

CheckBox app, mode=1, pos={5,165},value=0, title="Append to Top Graph", proc=sec12check

CheckBox rem, mode=1, pos={5,180},value=0, title="Remove from Top Graph", proc=sec12check

TitleBox title3, title="Select Plot Style", pos={5,200}, frame=0

CheckBox over, mode=1, pos={5,215}, value=1,title="Overlay Plot", proc=sec12check

CheckBox stac, mode=1, pos={5,230}, value=0,title="Stacked Plot", proc=sec12check

TitleBox title4, title="Select Which to Plot", pos={5,250}, frame=0

CheckBox saxs, mode=1, pos={5,265}, value=1,title="Plot SAXS", proc=sec12check

CheckBox waxs, mode=1, pos={5,280}, value=0,title="Plot WAXS", proc=sec12check

CheckBox swaxs, mode=1, pos={5,295}, value=0,title="Plot SWAXS", proc=sec12check

Button plot, pos={5,315}, title="Plot", proc=sec12but, size={80,20}

// Data workup section

Button convert, pos={5,335}, title="Convert", proc=sec12but, size={80,20}

Button lines, pos={5,355}, title="Add Lines", proc=sec12but, size={80,20}

End

// Handle all button events

Function sec12but(ctrlname) : ButtonControl

String ctrlname

//Convert button

if(stringmatch(ctrlname,"convert")==1)

sec12convert()

endif

//Load File buttons

if(stringmatch(ctrlname,"loadone")==1)

Sec12LoadOne("","")

endif

if(stringmatch(ctrlname,"loaddir")==1)

Sec12LoadDir("")

endif

//Combine button

if(stringmatch(ctrlname,"combine")==1)

sec12combine()

endif

//Update wave list

PopupMenu wavepick, value=Sec12getWaves()

//Plotting button

if(stringmatch(ctrlname,"plot")==1)

//Get the relevant variables from controls

String thewave="",y="",x="", curwave="", leg="", cursam="", curtype=""

Variable newval, appval, remval, overval, stacval, saxsval, waxsval, swaxsval

ControlInfo wavepick; thewave=S_Value

ControlInfo new;newval=V_Value

ControlInfo app;appval=V_Value

ControlInfo rem;remval=V_Value

ControlInfo over;overval=V_Value

ControlInfo stac;stacval=V_Value

ControlInfo saxs;saxsval=V_Value

ControlInfo waxs;waxsval=V_Value

ControlInfo swaxs;swaxsval=V_Value

//Get the correct wave names

SetDataFolder root:Sec12

if(saxsval==1)

y="Si"+thewave

x="Sq"+thewave

else

if(waxsval==1)

y="Wi"+thewave

x="Wq"+thewave

else

y="SWi"+thewave

x="SWq"+thewave

endif

endif

//Start plotting i guess.

//If new plot selected

if(newval==1)

//Print y,x

Display/K=1 $y vs $x

//Make the plot look nice

ModifyGraph log(left)=1,mirror=2,axThick=1.5,lblMargin=5,standoff=0;DelayUpdate

Label left "Log(Intensity) (a.u.)";DelayUpdate

Label bottom "q(Å\\S-1\\M)"

endif

//If append is selected

if(appval==1)

//Make sure there is actually a plot up

if(strlen(Stringfromlist(0,WinList("*",";","WIN:1")))==0)

//Same as plot new

Display/K=1 $y vs $x

//Make the plot look nice

ModifyGraph

log(left)=1,mirror=2,axThick=1.5,lblMargin=5,standoff=0;DelayUpdate

Label left "Log(Intensity) (a.u.)";DelayUpdate

Label bottom "q(Å\\S-1\\M)"

else

Appendtograph $y vs $x

//If stacked plot is selected

if(stacval==1)

//Find the new offset value

Variable num=1, j=0

do

curwave=WaveName("",j,1)


break

endif

j+=1

num=10*num

while(1)

//Apply the vertical offset

ModifyGraph muloffset($y)={0,num}

endif

endif

endif

//If remove is selected

if(remval==1)

Variable i=0

//Find the wave to remove

do



break

endif

if(stringmatch(y,curwave)==1)

//Remove the wave

Removefromgraph $y

endif

i+=1

while(1)

endif

//Chenge the plot colors and make the legend

i=0

do



break

endif

//Apply correct colors

ModifyGraph rgb($curwave)=(sec12R(i),sec12G(i),sec12B(i))

i+=1

//Find current sample name

if(stringmatch(curwave[0,1],"SW")==1)

cursam=curwave[3,strlen(curwave)]

curtype=" - SWAXS\r"

else

cursam=curwave[2,strlen(curwave)]

if(stringmatch(curwave[0],"S")==1)

curtype=" - SAXS\r"

else

curtype=" - WAXS\r"

endif

endif

//Add curent wave to legend

leg+="\\s(\'"+curwave+"\')"+cursam+curtype

while(1)

//Trim legend and apply to plot

leg=leg[0,strlen(leg)-2]


endif

//Add lines

if(stringmatch(ctrlname,"lines")==1)

sec12lines()

endif

End

// Handle all checkbox change events

Function sec12check(ctrlname, checked) : CheckBoxControl

String ctrlname

Variable checked

//Select Operation controls

if(stringmatch(ctrlName,"new")==1)

if(checked==1)



Button plot, title="Plot"

endif

endif

if(stringmatch(ctrlName,"app")==1)

if(checked==1)



Button plot, title="Append"

endif

endif

if(stringmatch(ctrlName,"rem")==1)

if(checked==1)



Button plot, title="Remove"

endif

endif

//Select Plot Style controls

if(stringmatch(ctrlName,"over")==1)

if(checked==1)

Checkbox stac, value=0

endif

endif

if(stringmatch(ctrlName,"stac")==1)

if(checked==1)

Checkbox over, value=0

endif

endif

//Select Which to Plot controls

if(stringmatch(ctrlName,"saxs")==1)

if(checked==1)

Checkbox waxs, value=0

Checkbox swaxs, value=0

endif

endif

if(stringmatch(ctrlName,"waxs")==1)

if(checked==1)

Checkbox saxs, value=0

Checkbox swaxs, value=0

endif

endif

if(stringmatch(ctrlName,"swaxs")==1)

if(checked==1)

Checkbox saxs, value=0

Checkbox waxs, value=0

endif

endif

End

Function sec12R(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 1:

case 8:

result=65280

break

case 3:

case 4:

case 5:

case 6:

result=0

break

case 7:

result=39440

break

case 2:

result=52224

break

endswitch

return result

End

Function sec12G(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 6:

case 7:

case 8:

result=0

break

case 1:

case 5:

result=43520

break

case 3:

case 4:

result=65280

break

case 2:

result=52224

break

endswitch

return result

End

Function sec12B(num)

Variable num

Variable result=0

num=mod(num,9)

switch (num)

case 0:

case 1:

case 2:

case 3:

result=0

break

case 4:

case 5:

case 6:

result=65280

break

case 7:

result=58880

break

case 8:

result=52224

break

endswitch

return result

End

// Convert file for use in Jade crystallography software for further data analysis

Function sec12convert()

String thewave="", y="", x="", t="", ti="",

win=StringfromList(1,WinList("Sector12Tools*",";","WIN:64")), name=""

//Get the wave

Variable saxsval, waxsval, swaxsval

ControlInfo/W=$win wavepick; thewave=S_Value

ControlInfo/W=$win saxs;saxsval=V_Value

ControlInfo/W=$win waxs;waxsval=V_Value

ControlInfo/W=$win swaxs;swaxsval=V_Value



if(saxsval==1)

y="Si"+thewave

x="Sq"+thewave

t="St"+thewave

ti="Sti"+thewave

name=thewave+"saxs"

else

if(waxsval==1)

y="Wi"+thewave

x="Wq"+thewave

t="Wt"+thewave

ti="Wti"+thewave

name=thewave+"waxs"

else

y="SWi"+thewave

x="SWq"+thewave

t="SWt"+thewave

ti="SWti"+thewave

name=thewave+"swaxs"

endif

endif

//Convert q to two theta

Wave wx=$x

Duplicate/O $x, $t

Wave wt=$t

wt=180/pi*asin(1.033*wx/4/pi)

//Modulate the intensity of a duplicate intensity wave for Jade importing

Duplicate/O $y, $ti

Wave newint=$ti

newint=newint*1000000

//Put waves in new table, format them for export and save

Edit/N=convert $x, $t, $ti

ModifyTable format($ti)=1, format($t)=3,digits($t)=6

Save/J/F/M="\r\n" $t,$ti as name

DoWindow/K convert

End

// Function to add diffraction lines to data for data analysis

Function sec12lines()


String/G xwave, ywave

String thewave="",win=StringfromList(1,WinList("Sector12Tools*",";","WIN:64"))

//Get the wave

Variable saxsval, waxsval, swaxsval

ControlInfo/W=$win wavepick; thewave=S_Value

ControlInfo/W=$win saxs;saxsval=V_Value

ControlInfo/W=$win waxs;waxsval=V_Value

ControlInfo/W=$win swaxs;swaxsval=V_Value



if(saxsval==1)

ywave="Si"+thewave

xwave="Sq"+thewave

else

if(waxsval==1)

ywave="Wi"+thewave

xwave="Wq"+thewave

else

ywave="SWi"+thewave

xwave="SWq"+thewave

endif

endif

Wave xs=$xwave

Wave ys=$ywave

String x2="x2"+xwave, y2="y2"+ywave, leg="\\s(\'"+y2+"\') "+thewave


Duplicate xs, $x2

Duplicate ys, $y2

Display/K=1/N=difflinesplot $y2 vs $x2

WAVE x2w=$x2

WAVE y2w=$y2

ModifyGraph log(left)=1,lsize=1.5,mirror=2,fSize=12,axThick=1.5;


Variable maxx=WaveMax(y2w),maxy

Variable i=0

do

if(y2w[i]==maxx)

maxy=x2w[i]

break

endif

i+=1

while(i<numpnts(y2w))

Variable L,C,S,G,start,low=0.0001,high=0.1

NewPanel /K=2/W=(100,100,400,450) as "Add Diffraction Lines"

TitleBox titleL, pos={5,5}, title="L=", frame=0

TitleBox titleC, pos={5,85}, title="C=", frame=0, fColor=(0,0,65535)

TitleBox titleS, pos={5,165}, title="S=", frame=0, fColor=(0,30000,0)

TitleBox titleG, pos={5,245}, title="G=", frame=0, fColor=(65535,0,0)

Slider slideL, limits={.0001,.1,0}, value=maxy, pos={5,20}, size={200,50}, vert=0, ticks=1, variable=L,

proc=sec12linesSlider

Slider slideC, limits={.0001,.1,0}, value=maxy, pos={5,100}, size={200,50}, vert=0, ticks=1, variable=C,

proc=sec12linesSlider, fColor=(0,0,65535)

Slider slideS, limits={.0001,.1,0}, value=maxy, pos={5,180}, size={200,50}, vert=0, ticks=1, variable=S,


Slider slideG, limits={.0001,.1,0}, value=maxy, pos={5,260}, size={200,50}, vert=0, ticks=1, variable=G,


TitleBox valL, pos={20,5}, title=num2str(L), frame=0

TitleBox valC, pos={20,85}, title=num2str(C), frame=0, fColor=(0,0,65535)

TitleBox valS, pos={20,165}, title=num2str(S), frame=0, fColor=(0,30000,0)

TitleBox valG, pos={20,245}, title=num2str(g), frame=0, fColor=(65535,0,0)

TitleBox titleL1, pos={240,20}, title="Lamellae", frame=0

TitleBox titleC1, pos={240,100}, title="Cylinders", frame=0, fColor=(0,0,65535)

TitleBox titleS1, pos={240,180}, title="Spheres", frame=0, fColor=(0,30000,0)

TitleBox titleG1, pos={240,260}, title="Gyroid", frame=0, fColor=(65535,0,0)

Checkbox checkL, value=0, pos={220,20}, title="", proc=sec12linesCheck

Checkbox checkC, value=0, pos={220,100}, title="", proc=sec12linesCheck

Checkbox checkS, value=0, pos={220,180}, title="", proc=sec12linesCheck

Checkbox checkG, value=0, pos={220,260}, title="", proc=sec12linesCheck

Button closer, pos={220,290}, title="Close", proc=sec12linesclose, help={"Close the diffraction lines tool

which will remove lines"}

Button markers, pos={220,320}, title="Markers", proc=sec12linesclose, help={"Close the diffraction lines

tool and leave behind markers where the lines where"}

SetVariable lowvar activate, limits={0.0001,1,0.0001}, size={100,20}, noedit=0, live=1,

value=_NUM:0.0001, frame=0, pos={10,320}, title="Low limit", proc=sec12linesLimits

SetVariable highvar activate, limits={0.001,1,0.001}, size={90,20}, noedit=0, live=1, value=_NUM:0.1,

frame=0, pos={120,320}, title="Highlimit", proc=sec12linesLimits

Sec12updateLines()

End

Function sec12linesclose(ctrlName):ButtonControl

String ctrlName


SVAR xwave=xwave, ywave=ywave

String y2="y2"+ywave, x2="x2"+xwave

Wave xs=$x2

String lamw,lamx,lamy,lamw2,cylw,cylx,cyly,cylw2,sphw,sphx,sphy,sphw2,gyrw,gyrx,gyry,gyrw2

//Checks to see if markers should be added before close

if(stringmatch(ctrlname,"markers")==1)

Variable lon, i=0, xval, j=0, con, lamnum, cylnum,sphnum,gyrnum, son, gon

//How many peaks of each morphology to mark, if 0 it means do them all

Prompt lamnum, "Number of Lam Peaks"

Prompt cylnum, "Number of Cyl Peaks"

Prompt sphnum, "Number of Sph Peaks"

Prompt gyrnum, "Number of Gyr Peaks"

DoPrompt "Input Peak Numbers", lamnum,cylnum,sphnum,gyrnum

if(lamnum==0)

lamnum=50

endif

if(cylnum==0)

cylnum=50

endif

if(sphnum==0)

sphnum=50

endif

if(gyrnum==0)

gyrnum=50

endif

//Add lamellar tags


if(lon>0)

lamx="lamx"

Wave lx = $lamx

do

xval=lx[i]

j=0

do

if(xs[j]>lx[i])

xval=j

break

endif

j+=1

while(1)

Tag/F=0/X=0/Y=5/L=0/TL=0/B=1/T=0.005 $y2, xval,"\\W523"

i+=1

if(i==numpnts(lx)||i==lamnum)

break

endif

while(1)

endif

//Reset index and add cylinder tags

i=0


if(con>0)

cylx="cylx"

Wave cx = $cylx

do

xval=cx[i]

j=0

do

if(xs[j]>cx[i])

xval=j

break

endif

j+=1

while(1)


i+=1

if(i==numpnts(cx)||i==cylnum)

break

endif

while(1)

endif

//Reset index and add spheres tags

i=0


if(son>0)

sphx="sphx"

Wave sx = $sphx

do

xval=sx[i]

j=0

do

if(xs[j]>sx[i])

xval=j

break

endif

j+=1

while(1)


i+=1

if(i==numpnts(sx)||i==sphnum)

break

endif

while(1)

endif

//Reset index and add gyroid tags

i=0


if(gon>0)

gyrx="gyrx"

Wave gx = $gyrx

do

xval=gx[i]

j=0

do

if(xs[j]>gx[i])

xval=j

break

endif

j+=1

while(1)


i+=1

if(i==numpnts(gx)||i==gyrnum)

break

endif

while(1)

endif

endif

//Change legend

String text1=""

if(lon>0)

text1+="\\W523Lamellae\r"

endif

if(con>0)

text1+="\\W522Cylinders\r"

endif

if(son>0)

text1+="\\W518Spheres\r"

endif

if(gon>0)

text1+="\\W507Gyroid\r"

endif

text1=text1[0,strlen(text1)-2]

Legend/C/N=text41/J/F=0/B=1/A=RC/LS=1 text1


KillVariables/A

lamw="lamw"

lamx="lamx"

lamy="lamy"

lamw2="lamw2"




endif

cylw="cylw"

cylx="cylx"

cyly="cyly"

cylw2="cylw2"




endif

sphw="sphw"

sphx="sphx"

sphy="sphy"

sphw2="sphw2"




endif

gyrw="gyrw"

gyrx="gyrx"

gyry="gyry"

gyrw2="gyrw2"




endif

String name="difflinesplot"

DoWindow/K $WinName(0,64)

DoWindow/C olddifflinesplot

End

// Handle diffraction lines events

Function sec12linesLimits(ctrlName,varNum,varStr,varName) : SetVariableControl

String ctrlName

Variable varNum

String varStr,varName

Sec12updateLines()

End

Function sec12linesSlider(ctrl,ctrlVal,event): SliderControl

String ctrl


Sec12updateLines()

End

Function sec12linesCheck(ctrl,val): CheckboxControl

String ctrl

Variable val

Sec12updateLines()

End

Function Sec12updateLines()


SVAR xwave=xwave, ywave=ywave

String x2="x2"+xwave,y2="y2"+ywave

Wave ys =$y2

Wave xs =$x2

Variable max1=WaveMax(xs)

Variable L,C,S,G,lon,con,son,gon,i,j,high,low

ControlInfo lowvar; low=V_Value

ControlInfo highvar; high=V_Value

ControlInfo slideL; L=V_Value


ControlInfo slideS; S=V_Value

ControlInfo slideG; G=V_Value





Slider slideL, limits={low,high,0}

Slider slideC, limits={low,high,0}

Slider slideS, limits={low,high,0}

Slider slideG, limits={low,high,0}

TitleBox valL, title=num2str(L)


TitleBox valS, title=num2str(S)

TitleBox valG, title=num2str(G)


lamw="lamw"

lamx="lamx"

lamy="lamy"

lamw2="lamw2"




endif


cylw="cylw"

cylx="cylx"

cyly="cyly"

cylw2="cylw2"




endif


sphw="sphw"

sphx="sphx"

sphy="sphy"

sphw2="sphw2"




endif


gyrw="gyrw"

gyrx="gyrx"

gyry="gyry"

gyrw2="gyrw2"




endif

if(lon>0) //Add lam diffraction lines if checked

Make lw={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20}

i=0

j=20

do

if(L*lw[i]>max1)

j=i

break

endif

i+=1

while(i<numpnts(lw))

i=0

Make/N=(j) lw2

do

lw2[i]=lw[i]

i+=1

while(i<j)

Duplicate lw2,$lamx,$lamy

Wave lx = $lamx

Wave ly = $lamy

lx=L*lw2

i=0

j=0

do

do

if(xs[j]>lx[i])

ly[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(lx))

rename ly, $lamy

rename lx, $lamx

appendToGraph/W=difflinesplot ly vs lx

ModifyGraph/W=difflinesplot mode(lamy)=1,rgb(lamy)=(0,0,0)

endif

if(con>0) //Add cyl diffraction lines if checked

Make cw={1,3,4,7,9,12,13,16,19,21,25,27,28,31,36,37,39,43,48,49,52,57,61,63,64,67,73,75,76,79}

i=0

j=30

do

if(C*cw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(cw))

i=0

Make/N=(j) cw2

do

cw2[i]=cw[i]^(1/2)

i+=1

while(i<j)

Duplicate cw2,$cylx,$cyly

Wave cx = $cylx

Wave cy = $cyly

cx=C*cw2

i=0

j=0

do

do

if(xs[j]>cx[i])

cy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(cx))

rename cy, $cyly

rename cx, $cylx

appendToGraph/W=difflinesplot cy vs cx

ModifyGraph/W=difflinesplot mode(cyly)=1,rgb(cyly)=(0,0,65535)

endif

if(son>0) //Add sph diffraction lines if checked

Make

sw={1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,

40}

i=0

j=40

do

if(S*sw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(sw))

i=0

Make/N=(j) sw2

do

sw2[i]=sw[i]^(1/2)

i+=1

while(i<j)

Duplicate sw2,$sphx,$sphy

Wave sx = $sphx

Wave sy = $sphy

sx=S*sw2

i=0

j=0

do

do

if(xs[j]>sx[i])

sy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(sx))

rename sy, $sphy

rename sx, $sphx

appendToGraph/W=difflinesplot sy vs sx

ModifyGraph/W=difflinesplot mode(sphy)=1,rgb(sphy)=(0,30000,0)

endif

if(gon>0) //Add gyr diffraction lines if checked

Make gw={6,8,14,16,20,22,24,26,30,32,38,40,42,46,48,50,52,54,56,62}

i=0

j=20

do

if(G*gw[i]^(1/2)>max1)

j=i

break

endif

i+=1

while(i<numpnts(gw))

i=0

Make/N=(j) gw2

do

gw2[i]=gw[i]^(1/2)

i+=1

while(i<j)

Duplicate gw2,$gyrx,$gyry

Wave gx = $gyrx

Wave gy = $gyry

gx=G*gw2

i=0

j=0

do

do

if(xs[j]>gx[i])

gy[i]=ys[j]

break

endif

j+=1


i+=1

while(i<numpnts(gx))

rename gy, $gyry

rename gx, $gyrx

appendToGraph/W=difflinesplot gy vs gx

ModifyGraph/W=difflinesplot mode(gyry)=1,rgb(gyry)=(65535,0,0)

endif

End

Computer Code for Materials Scientists: Igor Pro Procedures for Analyzing Dynamic Light

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Transcript of Computer Code for Materials Scientists: Igor Pro Procedures for Analyzing Dynamic Light