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NERS/BIOE 580
Lab02 - Introduction Module B

This module is intended to introduce the XSPECT utility programs, the database of xray interaction coefficients, and the collection of files defining the composition of various materials.

Discussion:

XSPECT utility programs are written in fortran and have been compiled for Microsoft Windows computers. The programs are distributed along with files for x-ray interaction data, material properties, detector tables, object dose tables, script procedures for building applications, and laboratory module instructions.

For Microsoft Windows systems, a binary Windows distribution of XSPECT should have been copied to the computer to be used as a part of 01-Intro-A and the tcl/tk script interpreter and the gnuplot plotting utility installed.

Task Intr-B1: Introduction to the lab documentation

The XSPECT files and programs are in $XSPECT_DIR/_xspect3.5. One of the subdirectories, _doc, contains files documenting each the programs and other important concepts. Change directories to _xspect3.5/_doc and review the documentation files named Material.txt and atten_coeff.txt.

Task Intr-B2: Introduction to material property files

The material definitions referred to in Material.txt are located in the directory $XSPECT_DIR/_materials. Look in this directory and examine a few of the materials. The files contain ascii text, but do not have a file extension. You will need to use the right button, select open, and use a text application such as notepad or wordpad.

Task Intr-B3: Script for XSPECT initialization, link.tcl

In the _xspect3.5/_tcl directory is a script used to initialize the XSPECT environment (link.tcl). Read the contents of this file and note the first few lines that contain the instructions to start the tcl/tk interpreter that were described in Tcl4xspect.pdf. The commands in link.tcl needs to be configured for the computer you are using and will then be used for later laboratory modules.

Task Intr-B4: Setting the XSPECT_DIR environmental variable

To obtain the directory where the executable programs are located, the link.tcl script obtains a base directory name that must be set as an environmental variable. The executable programs also use this base directory to locate various data files. For this reason, the directory structure of the files in the XSPECT distribution should not be changed.

For Microsoft Windows systems, environmental variables are set using the system properties available to the user. For Windows 7 systems, open the control panel using the start button. For Windows 10, open the control panel by typing 'control panel' in the search box on the taskbar. In the control panel, select 'View by: small icons', and select the 'system' option. In the left column, select 'Advanced system settings'. In the 'System Properties' window you will see a button for 'Environmental Variables'.

Create a 'NEW' system variable with a name of XSPECT_DIR and a value with the path to the _xspect3.5 directory. For example;

XSPECT_DIR    C:\XIRL\SRC\_Rad-Img

Note: the Windows operating system uses a back-slash to separate the sequences of folders in a path.

If you do not have account privileges to set environmental variables on the system you are using, there is an alternative method. In the _xspect3.5/_tcl/link.tcl file, add the 'set env(XSPECT_DIR) ..' command shown below just before the 'set BIN' command;

set env(XSPECT_DIR) "C:/XIRL/mikef/SRC/_Rad-Img"
set BIN [file join $env(XSPECT_DIR) _xspect3.5 _bin]

The path in quotes should be the path to the course distribution that you have installed on the system you are using.

Note: Unlike Windows, Tcl/Tk uses a forward-slash to separate the sequence of folders in a path as does Unix/Linux and MacOS. Remember to use the forward-slash as Tcl/Tk treats the back-slash as an escape indicator to skip the next character except for certain special characters like \n for newline.

Task Intr-B5: Starting a tcl/tk command window using link.tcl

On a Microsoft Windows system, the tcl/tk interpreter is run interactively by starting the 'wish' program from the programs menu. This creates a command window that will interpret either tcl or tk commands along with a window to place graphic widgets. An alternative interpreter, tclsh, will only recognize tcl commands.

To interpret commands that have been saved in a file, Windows executes files with extensions of .tcl using the wish interpreter. This property is set when tcl/tk is installed. Simply executing the file (double click) will run the wish program and sequentially interpret each command in the file.

The _xspect3.5/_tcl/link.tcl script will be used at the beginning of scripts assembled in subsequent laboratory modules. In the _xspect3.5/_tcl/link.tcl script, the platform is determined as Windows or Unix and the configuration adjusted accordingly. For windows, the command 'console show' is used to allow the interactive tcl/tk command interpreter window to be used to report messages or execute additional commands.

For Windows systems, the appropriate gnuplot application is defined in _xspect3.5/_tcl/link.tcl as wgnuplot.exe using a path typical of that for gnuplot installation. Check this to see if it is correct for your installation. If not, the full path needs to be set by editing the 'set gnuplot ..' command located located just after the 'console show' command. For example,

set gnuplot [file join C:/ {Program Files} gnuplot bin wgnuplot.exe]

Note: The 'file join ..' command within the [..] brackets combines the arguements into a path appropriate for the OS being used. If a path element has spaces, it needs to be enclosed in {..} brackets. In this example {Program Files} denotes the folder in a 32 bit system. For a 64 bit system it will be {Program Files (x86)}.

At the end of the _xspect3.5/_tcl/link.tcl program are simple commands to pack a button in the graphic window that quits the wish interpreter. Later applications will expand these graphic commands.

Make a directory in your home folder or desktop with a name such as NERS580. This can be used for completing the lab module assignments. Then place a copy of the _xspect3.5/_tcl/link.tcl file that has been modified to initialize your XSPECT environment and place it in the NERS580 home directory. Running this script will open a command window that can be used to execute XSPECT commands.

The program atten_coeff produces a table of linear attenuation coefficients and a table of material transmission values. Using the above link, review the atten_coeff documentation. Then start the interactive interpreter using the link.tcl script in the NERS580 home directory and define input arguments for 1 cm of Aluminum and 1 mm of Lead;

• set erange "10 50 2 \n"
• set matsN "2
•           al_1100 1.0
•           lead 0.1 \n"
• set in "$erange $matsN"

The arguments have been defined as two variables, erange and matsN, only for clarity. Note that a newline character has been included at the end of the text strings defined for both variables.

The program can now be executed by entering the following command at the interpreter prompt;

• exec $BIN/atten_coeff << $in

Files labeled al_1100.atn, lead.atn, and trans.dat will be created in the same directory as link.tcl.

Similar commands are in the file _templates/atten_coeff.txt where the atten_coeff program is executed using the Tcl catch command to report any execution errors. Copy this file to the NERS580 home directory. The arguments can be modified to match the material and thicknesses of interest. The template commands can then be executed using the Tcl source command. In an interactive tcl/tk interpreter window started with link.tcl, enter the following command;

• source atten_coeff.txt

For this laboratory, select a material and generate attenuation results for an appropriate thickness. I would suggest using an energy range from about 10 to 100 keV. I would further suggest selecting a material with a high Z element in it so as to see the K absorption edges. Use a dKev of about 1 so the the edges appear distinctly. Be sure the thickness you chose gives reasonable transmission values.

Using a gnuplot command file, plot the mass attenuation coefficient for the material from the *.atn file and save it as a png graphic file. You will need to use the "using 1:3" option for the plot;

• gnuplot> plot datafile using 1:3 ...

Next, modify the gnuplot command file to plot the total transmission from the trans.dat file and save it as a png graphic file. The gnuplot help file and the gnuplot overview document, 'Gnuplot4xspect.pdf', will explain how to set the line type to a solid line and put labels and titles on the graph. For the plot of attenuation coefficients you will want to use a semi-log plot by setting the y scale before the plot command;

• gnuplot> set logscale y

Save copies of these two plots for submission to the instructor.

Observe from these plots the features associated with K edge absorption and the strong energy dependence associated with the photoelectric cross section. Note in the transmission plot how the transmitted flux increased for energies just below the K edge.

Lab02 results:

For this module, simply turn in the plots of attenuation and transmission generated for the material that you selected.

• L02-B6-atn.png : Plot of material x-ray attenuation.
• L02-B6-trans.png : Plot of material x-ray transmission.

L02 Reference script: Lab02_Intr-B.tcl

Next:

The next module is 03-Source-A.