Edit Mode and Using the SampleId VAMAS Field

VAMAS blocks containing spectral data appear in the right-hand-side of the Experiment Frame window in CasaXPS. Initially, the organisation of these VAMAS blocks depends on the assignment within the VAMAS block of the numerical experimental variable VAMAS field and the species/transition VAMAS text-fields. Following the release of CasaXPS version 2.3.0, the organisation of the VAMAS Blocks, when displayed in CasaXPS, can be altered by means of the SampleId VAMAS text-field using the Edit Mode toolbar button.

The problem addressed via this new mode of operation for the right-hand-side of the Experiment Frame relates to data for which quantification between narrow scan spectra is not well-defined by the numerical values assigned to the individual VAMAS blocks. That is to say, situations where it is desired to align rows of spectra for quantification based on sample position, say, rather than an experimental variable such as temperature or pressure. The problem is that measurements at a given temperature may have been made for different samples on a sample bar and therefore aligning the VAMAS blocks with respect to the temperature, for example, would not position the VAMAS blocks appropriately for quantification of the individual samples. The new method for addressing this problem is to align the VAMAS blocks within the Experiment Frame using the text strings assigned to the SampleId VAMAS field. When the Edit Mode toolbar button is pressed, in addition to allowing the row labels to be edited, the VAMAS blocks are aligned by row using the SampleId. Pressing the Edit Mode toolbar button a second time returns the right-hand-side of the Experiment Frame to the display alignment based on the experiment variable. Columns of VAMAS blocks are separated in the same way as earlier releases of CasaXPS using the combined strings assigned to the species/transition text-fields.

All these numerical and text VAMAS information can be adjusted within CasaXPS, thus permitting the data to be aligned appropriately for quantification. The toolbar buttons in Figure 1 represent the options for making such adjustments.

Figure 1: Toolbar buttons from the second toolbar used to adjust the display mode for the VAMAS blocks in the right-hand-side of the Experiment Frame.

VAMAS block alignment is switched between experimental variable and SampleId by pressing the Edit Mode toolbar button.

The SampleId and BlockId text-fields for a selected set of VAMAS blocks are altered using the dialog window under this toolbar button (Figure 2). The dialog window in Figure 2 will set the SampleId and BlockId for those VAMAS blocks selected prior to invoking the toolbar button, provided the appropriate tick-box on the dialog window is ticked when the OK button is pressed.

Figure 2: VAMAS file displayed in CasaXPS where the experimental variable is not relevant to the logical structure of the data. The dialog window displayed over the VAMAS blocks allows the SampleId to be set for groups of VAMAS blocks selected in the right-hand-side of the Experiment Frame.

Once the SampleId has been set appropriately for the data in a VAMAS file, the Edit Mode toolbar button can be pressed, the result of which is the VAMAS blocks are realigned to reflect the SampleId fields. All VAMAS blocks with distinct Species/Transition fields will appear on the same row within the Experiment Frame (Figure 3).

Figure 3: Alignment of the VAMAS blocks following pressing the Edit Mode toolbar button.

An alternative means of editing the SampleId field is via the row label visible when in Edit Mode. The text-fields can be edited by double-clicking the individual row labels. Once a label is edited, a dialog window appears, which asks if the SampleId for the corresponding row should be adjusted too. If the SampleId is altered, the VAMAS blocks will be reordered using the new information entered via the row label. Since the row label will require re-initialising (VAMAS blocks may have moved), a further dialog window offers the means of re-initialisation using either the SampleId strings or the first line of the VAMAS block comment. The choice appears for historical reasons and for new data the SampleId is almost certainly the desired method.