Contents of Chapter.
The menu item File controls various kinds of input-output and related features for files.
These items enable the user to convert foreign spectrum files to the DTSA internal binary form. With any selection you are requested to supply the name of the file to convert and a name for the DTSA File. Some of the foreign files do not supply any or all of the information that can be stored in the DTSA File Headers. You may complete the Header information in the DTSA File as described in the section under Headers. Be sure to check the detector specifications for these files as that information is usually not passed in the file header.
NOTE!!! Since any number of files (spectra) may be stored in one DTSA file, be sure to name the receiving DTSA file FIRST. Then we ask the user to find and open the ASCII file(s) to be converted. You can then add all the desired ASCII spectra to the DTSA binary file. All spectra in a DTSA file MUST be at the SAME BEAM VOLTAGE. After all files are processed, you can view them by clicking through the file by use of the file control arrows just below the KLM markers in the MAIN CONTROL WINDOW. If a spectrum has been inadvertently included, or there is some other reason to want it removed, then this can be done in the Spectrum Headers Menu Item.
Read ASCII Column: Converts a single ASCII file in which the spectrum counts are stored in simple column format with no header information. The column can be any length up to 8192 entries either in a single column or in multiple columns. The allowed delimiters are a space, a tab or a CR. DO NOT include a column of energies or channel numbers.
All of the currently available Plug-ins are included. If you have a different format, please contact us. Most of the formats are ASCII as these are the easiest to convert.
This menu item brings up a dialog that allows the conversion of display spectra to an ASCII file in a format accessible by four commercial programs. Either only the spectrum in WORK or all displayed spectra can be written to the ASCII file with each selected spectrum in one column of the file. All the files have the same tab delimited format, but DTSA assigns the appropriate file "creator" and icon to each type. This enables simply "double clicking" the icon to start the appropriate application. Most spreadsheet programs will open and read any of the files if the spreadsheet program is started and then the files are opened by the program.
This function operates on the "Work" spectrum. When this selection is made, the standard Mac file-saving dialog shown above appears. When Save is selected to exit the dialog, the Experiment Header information, the Spectrum Header information and spectrum counts are written to the DTSA File that the user has created. To supply or edit the header information, see the sections describing the Headers under Headers in the Menu Bar. Any other spectrum in Work, with the Spectrum Header, may be appended to this file by using the Save Work button that can be found on the left side of the Control Window. A file can be appended until a new DTSA File is created using the button Save DTSA Spectrum to Disk.
Spectra may be appended to an old DTSA file by selecting this menu item. It brings up the standard file open dialog to allow the user to select the DTSA file to open for appending. This file will then be opened in the same manner as the Save DTSA to Disk so that additional spectra may be appended by clicking the Save Work button in the Main Control Window. Be sure that the spectrum to be saved has the same Experiment Header information as the selected DTSA file.
This menu selection activates the Mac file selection dialog.
From the list displayed, you may select an old DTSA File to open. The first spectrum in the file will be displayed in "Work". To get a list of the spectra in the file, click the Scan File button in the Main Control Window.
These items are for creating, appending, and displaying files of DTSA references. References are used in linear least squares fitting of spectra to determine the areas of the families of characteristic lines. A reference is usually obtained from a spectrum with high counts (>10,000 counts in the peak area) that has been background subtracted so that the distribution of counts goes smoothly to zero on each side of the family of lines to be used as a reference. All families of lines with no overlap from another element may be saved from Work as references. The concentrations of the elements in the specimen from which the spectrum was obtained need not be known. All references useful for a particular type of analysis should be saved to one file: a file of references for biological specimens, for steels, etc. The structure of a reference file is similar to a spectrum file. It has an experiment header that is obtained from the experiment header of the spectrum of the first reference saved to the file, and each reference has a header. All the references in a file must share certain experimental parameters: the beam energy (keV), the detector type and resolution, and the energy increment (eV) per channel. Any reference may be copied to other reference files, but only one reference for each family can be saved to a file. When adding a reference to a file, the program compares the experiment header of the spectrum to that of the reference file and flags a disparity to the user. The program also searches the file for a reference already saved for the family, displays the old reference in RESULTS, and prompts the user to either keep or replace the old reference.
I. Calibrate your analyzer system. The references to be made will then be valid as long as this calibration remains valid. Copper, or an iron silicate such as Fayalite are particularly good for this purpose and may also be used for an accurate determination of detector resolution. Edit the fitted value for detector resolution into the header: See Simplex and Calibrate .
II. Acquire a spectrum with very high counts (>10,000 counts in the peak area) for the peak for which a reference is to be made: Fill in the Header information.
III. Background subtract the spectrum using Background Subtract in the Math menu until the families of lines to be saved as references go smoothly to zero on the low and high energy sides. It may not be possible to achieve this for more than one family at a time. Rotate Wk & Reslt: See Background Subtract .
IV. Click ROI, and Peak Wipe each useable family to include a few zero count channels on both sides of a family: See ROI (Regions-of-Interest).
V. Under Main Menu File, MLLSQ References select New File. If there is more than one Peak ROI set, the program flags the user to check that they are all for spectrum segments useable as references. The program then asks the user to verify that the beam energy (keV), resolution and eV per channel from the WORK Header are correct. If so, a dialog to name the new reference file is displayed. Supply a name and click Save.
VI. The Elements dialog is displayed: check the elements for which there are Peak ROIs set. The WORK Experiment Header is copied to the reference file and each reference distribution is stored with its header information.
I. Under Main Menu File, MLLSQ References select Display Ref. The file selection dialog is displayed: double click the file to be displayed or click the file then Open. The display reference dialog is activated.
II. Input the family name of the reference to display in WORK, then click OK to retire the dialog. If the reference is not in the file a message will be displayed. Or check the box to select from a list of references in the file, then click OK to retire the dialog. A scrollable list of references in the file is displayed: double click on a selection to display the reference or click Quit to retire the list.
III. Once a reference file is opened to display a reference, the arrows and buttons for Spectrum Number may be used to move through the file.
I. Prepare a spectrum as in steps I - IV under Making a NEW Reference File.
II. Under Main Menu File, MLLSQ References select Add Ref. The file selection dialog is displayed: double click the file to be appended to or click the file then Open.
III. The experiment headers of the reference file and the spectrum file are compared and the user is flagged and appending terminated if there is a difference between any two of the critical experiment parameters.
IV. The file is searched for the family to be saved. If a reference for the family is not in the file, the new reference is appended to the file. If there is a reference for the family in the file, the old reference is displayed in RESULTS and a dialog prompting the user to KEEP or REPLACE the reference is displayed. Click OK to dismiss the dialog.
The options under this selection allow the user to manipulate DTSA Fit Files. Rename a File bring up the Mac file selection dialog to pick the file to rename and then the Mac save file dialog to input the new name. This is useful for renaming the default Fit File that is written when the MLLSQ or Simplex fitting procedure is run and a filename has not been supplied for the results. Output Options brings up a dialog to create the ASCII files checked from the selected binary Fit File. Show Contents brings up the Mac file selection dialog and then displays an ASCII output of the binary Fit File selected. Open to Append brings up the Mac file selection dialog. The results of fitting a DTSA File are then added to the selected Fit File when Add Fit in the Main Control Window or Fit the File of Spectra under Analysis is selected.
DTSA has a great variety of options such as color schemes, choice of x-ray cross-section, take-off angle etc., which will customize the program to the preferences of the user(s) and their electron column instrument(s). DTSA can save the values for a particular configuration as a binary file. For example, one Preferences file might be for an SEM that has a take-off angle of 30 degrees. The second Preferences might be for a 200 keV AEM with a 23 degree take-off angle. Three pre-named files called "Preferences.mca", "Preferences1.mca", and "Preferences2.mca" are provided. The first is the default file to which a configuration is saved at program termination and existing data is overwritten. The default file is automatically read by the program at start-up and the saved configuration is restored. It should be noted that program termination means that you have quit DTSA and not experienced a power failure or a program crash. "Preferences1.mca" and "Preferences2.mca" are written or read at any time by selecting Values to Prefs1 etc., The first two hierarchical menu items bring up Mac file dialogs for selecting or creating a file of preferences with a user-supplied name.
The pre-named Preferences files are always written at the same "level" as DTSA, that is, they are in the same folder as DTSA.
NOTE The Preferences files save the spectrum that is in work at the time they are created. Consequently, when read, they will replace the spectrum in work. They do not, however, open a DTSA file; the active file remains active and can be restored to Work by using the Scan File controls.
A WARNING If you have inadvertently put a lot of extraneous values into the program variables by experimenting with procedures unfamiliar to you, or you have activated a bug that did some damage, the default Preferences file, Preferences.mca, will remember the damage and/or extraneous values and reactivate it on start up. It is always a good idea to save a Preferences file that will configure the program just the way you want it and working correctly. If the program seems to be broken, activate a good Preferences file or QUIT, throw away Preferences.mca, and start over.
This selection displays the dialog (shown below) that is used to choose distinctive colors for the various items in the Spectrum Display Window. Additionally, as an aid in printing displayed spectra to a non-color printer, it is possible to choose plotting symbols. It should be noted that the fastest screen refreshing is done when a single pixel-Connected combination is chosen. The currently active colors for each item are shown beside that item. The "Set Default Colors" button will reset any changed colors to the initial colors stored in the program. Color changes made by the user are saved in the Preferences File that is automatically saved when you Quit the program. The "No Header on Printout" check-box allows you to suppress printing the spectrum header on a printout.
When a color choice button is pushed, the following standard Macintosh color picker dialog will appear. The square color box at the top left will display the active and proposed colors.
The font size of the peak labels may be set to a larger size particularly for print-outs of spectra. Then if the printed spectrum is reduced in size, the peak labels will still be legible.
Spectrum printing in the DTSA program is particularly convenient because it is the Spectrum Display Window that is sent to the printer. The printed spectrum looks like it does on the display and so can be configured using the standard spectrum display controls and buttons. Some selected Header information is also printed below the Spectrum Display Window. It is possible to suppress the header - see Display Options above. The KLM markers may be printed along with any peak labels.
The selection Set-up Printer w/o Printing enables the user to prepare the printing configuration at any time. Clicking on the selection displays the Macintosh LaserWriter PageSetup dialog. To print spectra with a thinner or thicker line use a "Reduce or Enlarge" number other than "100". The plot size will remain the same but the "pen" size will change. Try numbers from 60-400. Thicker lines are useful for making viewgraphs and slides. If this dialog is accepted, the LaserWriter printing dialog is displayed. Once this dialog is accepted the printing configuration remains active for any spectrum printing but printing does not occur until one of the next two selections is chosen. Print 'Displayed' Spectra (those spectra that are selected for display) causes only the current screen display to be printed. Print all Spectra in active 'DTSA' file causes each spectrum in the DTSA File to be loaded into work and displayed and printed in turn with the same parameters as those active when the selection is made. Since the intensity of the highest peak in each spectrum may vary through the file, the vertical scale should be carefully chosen so that each spectrum is printed in a useful way.
Warning!! Some laser writer print dialog windows support gray scale and color and DTSA only prints black & white. This option must be off or the time to print will increase considerably. A typical example of print time, for the older Laser Writer Plus, is one minute from the print request to paper delivery. DTSA should become free from the print request in 20 seconds. In all cases, printing should occur as each print request is made.
TIP: In the print window, you can send the print image to an Encapsulated Postscript File instead of the printer. This file can then be imported into any document and printed as a part of the document.