Software Manual Section 12

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Setup 3 for Isotopic Measurements
	Introduction If you make several measurements with the same basic setup, this window is the one that you will always come back to. (Setup windows 1 & 2 only show up once.) Here we set things that might change for different measurement spots: stage position, file name, sample description. You can also define certain "stop conditions" that will cause the program to abort immediately should they come up.
	Number of Runs In the previous setup windows the number of blocks and cycles were defined. Here, the number of runs can be chosen. The main difference between adding more blocks and adding more runs is that each run is a separate measurement. While the results from any number of blocks will be saved in one set of data files, each run gets its own set of data files with different filenames for each run (see below). In addition, it is possible to move the sample stage automatically between runs.
	Measurement Time Display Here should be a display of the estimated measurement time for one run and the whole measurement. Not yet implemented.
	Data Files Up to three data files in different formats can be produced with each run. To simplify the file naming, everything starts with a 'base name'. This base name is supposed to describe the measurement in short. The base name can have spaces and funny characters which will be stripped automatically before the base name is converted into a valid file name.
	Data File Directory The directory where the data files are to be saved has been chosen in the setup window 2 already. It cannot be changed at this point and is only diplayed for reference.
	Data File Formats and Names There are three different formats for the data files from isotope measurements. At least one of these formats has to be selected at all times. File names cannot be chosen individually, but are assigned based on the 'base name' entered earlier. Old (HP) Format: This file format tries to duplicate the data files that were produced by the old HP computer. Data files in this format show only a limited amount of information about the measurement. However, it is possible to use the old UNIX-based data processing routines that were written for the old format. It may be useful to create data files in this format in the beginning, but this format should not be selected exclusively. Files in this format have names beginning with 'hp_': New Format: Data files in this new format contain much more informatin about the measurement than the old files ever did. It will be possible to reconstruct almost the entire measurement with the data contained in this file. Thus it will be possible to retroactively eliminate outliers that were due to electronic problems. It is advisable to always save the data in this format. Of course the file size of data files in this new format is bigger than in the old format, but this should not pose any problems. Files in the new format have the simplest names: Verbose Format: And finally ther is the verbose format, which goes one step further than the 'New Format'. Data files in this format contain detailed informatin about every single step during the measurement. Basically, a data file in this format records all the steps in the format they are shown in the 'Analysis Record' window (see section 14). Data files in this format use even more space to store and are useful mostly for debugging purposes. Verbose files have names beginning with 'vb_':
	File Names For Multiple Runs The file names generated are automatically coded for multiple runs. If a 'base name' of X and a measurement with 3 runs is chosen, the files will be names X_01.txt, X_02.txt and X_03.txt. (The .txt extension is added to make life easier on PCs which have a hard time with unknown files.) If only one run is chosen, the file name does not get a numbered extension in the middle, but will simply be called X.txt. Note: Even when only one run is chosen initially, there will be a pre-selected file name for a second run. The reason for this -seemingly odd- feature is that it is always possible to add more runs during the execution of the measurement. In case the number of runs is changed from 1 to 3 during the first run, the data files created will have the names X.txt, X_02.txt and X_03.txt (i.e. there is no X_01.txt in this case).
	Invalid Filenames The program checks whether the file names chosen are valid. In case a file with the given name already exists in the data directory chosen, a red 'Error' flag will show up right behind the invalid name. Modify the 'base name' to create new, unique file names. As long as at least one red 'Error' flag is shown, the 'Start Measurement' button will be dimmed out and disabled.
	Measurement Type Select here whether the current measurement is on a sample or on a standard (or neither). This selection has absolutely no effect on the measurement, but the some of the data files will show this information.
	Measurement Description Add a short description of the measurement or the sample here. If this field is empty, the 'base name' will be entered automatically.
	Stage Movement If 'Move Stage After Each Run' is checked, the step sizes for x and y (in microns) can be entered here. For information, the current position is shown here, too.
	Mass Peaks To Be Tracked The peaks that are to be tracked automatically during the measurement have already been selected earlier in setup window 2. While those are the default settings, it is possible to change these settings here for only the runs that are started now. This may be useful in cases where several measurements on standards and samples are made with the same basic measurement conditions, only that the automatic peak centering will be changed in some cases. To change the selections back to its default setting (from setup window 2), click on the 'Reset' button. To temporarily override the previous settings, click on the 'Change' button and then make the necessary changes in the window that pops up: Here, all the mass peaks with a bullet in front of their name are the ones to be tracked (both peaks in this case). To select or deselect an individual peak, click on its name. To select all or none, click on the corresponding buttons below. To reset the selection to its default, click on 'Reset'. To return to the main window, click on 'Exit'.
	Stop Conditions These are conditions under which a measurement should be aborted automatically. Useful in casese where the measured sample sputters away under the ion beam. These stop conditions are not yet implemented.
	Manual Calibration Before the first run the peak positions should be calibrated manually. There are three different options: All Peaks: Perform a manual calibration for every peak that is being measured. Track Peaks: Only calibrate those peaks manually, that are tracked automatically during a measurement. None: Do not calibrate any peaks manually. Choosing this option is not usually a good idea, unless 'Start Measuremnt With Positions From Previous Run' is selected (see below).
	Previous Peak Positions Choose this option to start the manual calibration (or the measurement, if no calibration is selected) with the positions from the previous run. This option is dimmed out and disabled if there was no previous run with the same setup or if you went back to setup window 2 between measurements.
	Print Options It is possible to get various measuremtent reports on the ThinkJet printer. The options are: Nothing: The environment-friendly option. General Setup (1st Run) & Detailed Run Results: This is the most detailed print option. It includes a full page of measurement setup information and one additional page per run with individual block results. The general setup will only be printed once (1st run). General Setup (1st Run) & Short Run Results: Here we get the full general setup information, but only limited data from each run. The results of each run are summarized in only 2 lines of text. Detailed Run Results: Detailed block results for each run, but no general setup information. Short Run Results: Only the 2 lines of text with run summary and no general setup information. Keep in mind that even when there is no printout, the complete measurement information is included in the 'new format' data files and can easily be retrieved from there, i.e., don't kill any trees you don't have to!
	Abort ISO To abort or exit the current setup for an isotopic measurement, click here.
	Back Click this button to return to setup window 2.
	Start Measurement Click here to start a measurement. This button may be disabled if some file names are invalid (see above).

FJ Stadermann	Back to Top	Next Section