Data Display and Browser *

Casa XPS is a multiple document interface (MDI) as defined by Microsoft. That is, it conforms to the same style as programs such as Microsoft Word or Excel and therefore presents each file (Document) with a document view. The main frame of the program manages a set of document/file frames. These file frames may be minimised or maximised, or arranged using the Window menu allowing the frames to be tiled with respect to one another or to create additional views of the same file.

The files in the case of Casa XPS are VAMAS files and are viewed through a splitter window. The right-hand view represents the logical structure of the experiment; showing the relationship of the spectra to each other and to the experimental variable. Data held within a VAMAS file appears in rows and columns, each row corresponds to data acquired under the same experimental variable value while the columns correspond to spectra resulting from measurements of the same chemical species and transition. The mouse is used to select a set of one or more VAMAS blocks from the right-hand side view and the data is displayed by selecting one of the two right most toolbar buttons in Figure 1.

The first icon will display a scrolled list of spectra one per tile. The second of the two allows spectra to be overlaid in the same tile. The remaining buttons are used to zoom into a region of a spectrum under mouse control.

Each VAMAS file requires at least one document frame. These are created using the "New" option on the file menu. Once an empty document is selected, the "Open" option from the same menu offers a File Dialog window for choosing the VAMAS file.

The browser view (right-hand-side splitter window) offers the data as described above. Selecting the data is achieved via the mouse in combination with the "Shift" and "Ctrl" keys. Positioning the cursor over a name in the browser view then clicking the left-hand mouse button selects that VAMAS block. If a range of contiguous blocks are required (as seen in the browser view), then select the first block in the range, followed by holding down the "Shift" key and selecting the last name for the range. All blocks between the first block and the last will be selected. The range selection works across columns as well as within rows or columns. That is to say, rectangular sets of block can be selected by this mechanism.

Additions to the current selection require the use of the "Ctrl" key. If the "Ctrl" key is held down and a new name is selected, the existing selection is retained in addition to the block just chosen. If the block indicated with the mouse is already selected then it is removed from the current selection. The "Shift" key and the "Ctrl" key when used together allow rectangular sets of blocks to be added or removed from the current selection.

Selecting a block without the use of the "Shift" key or the "Ctrl" key clears the current selection and replaces it by the indicated block.

Once a spectrum has been entered into the left-hand side scrolled display window the data can be examined under mouse control. In order to zoom into a range of the data, the mouse is used to mark a rectangular region and then the third button is pressed (Figure 1). The result of this action is to cause the graph axes to be computed from the defined area and the data is redisplayed. Zooming may be performed a number of times and the system maintains a list of zoom states. These zoom states can be revisited using the fourth toolbar button. To reset the list of zoom states press the fifth toolbar button. The axes are returned to the state when the data was first displayed in the scrolled list.

A printed page corresponds to the visible area associated with the left-hand scrolling window. Each click within the scroll bar moves the display by one page whilst dragging the scroll button allows the pages to be moved at will. The arrow buttons on the scrollbar permit fine adjustments to the position of the spectra in view.

Pages can be divided into sub units referred to as tiles. The format for the page is defined using a dialog window available from the main frame menu headed "Options". If "Page Layout" is selected, the dialog box presents property pages that allow the user to choose the number of tiles per page as well as how many rows and columns of such tiles should appear on the page. These pages represent an initial format for the number-of-tiles per page; however, the user is at liberty to adjust these as seen fit.

There is a maximum of sixteen tiles per page. The layout is specified by selecting the number of tiles to appear in, what is referred to as the major direction, then for each of the chosen number of major directions the user may select up to four tiles per minor direction. Since there are at most four major directions the limit of tiles per page is sixteen. A third option allows the user to choose whether the major direction corresponds to rows or columns of tiles. This permits the layout to be transposed at a click of a button.

Figure 2: Main Toolbar

Figure 2 shows the Main Toolbar. The dialog boxes available from the main menu "Options" are also displayed using buttons on the Main Toolbar. Move the cursor over a toolbar button; a hint describing the action associated with the button will popup.

Problem: The first release of CasaXPS limits the number of pages that can appear in the scrolled view. Although the modern PC hardware is 32-bit, some 16-bit code still remains, in particular the class used by the routine that sets the scroll bar attributes, does not like the logical scrolled area to exceed the range of a signed 16-bit number. Sorry! If more tiles are required to view a set of spectra, then the page layout mechanism can be used to reduce the overall size of the scrolled list.

Many of the attributes for displaying the spectra can be adjusted. The menu item labelled "Tile Display" on the "Options" menu displays a dialog window for modifying the appearance of the spectra.

Ranges for the axes, labels and fonts used for the labels can be adjusted on the first two property pages found on the "Tile Display" dialog window. The user may also choose between displaying the spectra using binding energy or kinetic energy, as well as counts per second or recorded counts.

An option on the "Y Axis" property page allows overlaid spectra to be offset with respect to one another. A check box enables the offset mechanism and a numeric-field permits a percentage to be entered which changes the separation of the traces. Other check boxes offered on the "Y Axis" property page alter the appearance of the display. The axis label and scale may be toggled on or off; also a spectrum may be plotted with the value of the experimental variable displayed at either side of the graph area.

An alternative way of displaying overlaid spectra is via the "Geometry" property page. Here the user can select between 2-D and 3-D views of the spectra. The latter option plots the spectra as a function of the experimental variable. The first spectrum in plotted in the front plane of a cube while the last spectrum in the selection is plotted at the back plane. All spectra in between appear at a plane that is determined from the value of the experimental variable for the VAMAS block.

The 3-D plot is adjusted using parameters that shift and scale the two planes associated with the front and back of the cube. Figure 3 shows a set of spectra plotted against etch time. The front plane is 75% of full size in both X and Y directions, while this reduced axes area has been shifted left by the maximum amount by specifying –100% for the shift. Note that the front plane can only be shifted around in X while the back plane may be shifted in both X and Y.

A third option for data display allows a set of spectra to be viewed in terms of abstract factors. This involves performing a Principal Component Analysis (PCA) on the spectra. Please see the section on Principal Component Analysis for a description of PCA and the use of this display option.

Other information drawn on a tile can be changed through the "Display" property page. The font and text for the title of a tile may be adjusted. The optional header information font may be changed similarly. A range of optional display items can be toggled on/off allowing the spectrum to appear, for example, with or without quantification regions present.

The "Colours" property page provides the means to set the colours used throughout the system. Spectra, backgrounds to spectra, synthetic components, regions and residual plots may have the colours adjusted. Fill colours used to display 3-D plots are also changed through the options on this page.

Selecting a button on the "Colours" property page brings up a dialog window that allows the existing colours to be viewed and new values set. In the case of spectra, sixteen colours may be chosen. These colours are displayed in the "Custom color" section of the dialog window and changed using the "Define Custom Colors" expanded form of the dialog window. To change a colour within the "Custom Color" set, first click on the colour you wish to change, then select a new colour, either from the default palette or using the colour values on the expanded section of the window. On pressing the button labelled "Add to Custom Colors" the colour square first selected is set to the colour just defined. Each colour subsequently specified and the "Add to Custom Colors" button pressed will cause the next custom colour cell to change. The cells are updated in a top to bottom, left to right order. However, the colours assigned to the graphs are assigned on a left to right, top to bottom order.

Some colour selections are for a single colour. In these cases, clicking on any colour cell, so that the focus box surrounds the intended cell, followed by selecting the "Ok" button on the dialog window will activate the "Apply" button on the property sheet for the tile parameters. The colour changes only take effect when the "Tile Display" window is applied, either by the "Ok" button or the "Apply" button.

Fonts are managed in a similar way to colours. Buttons are provided for fonts associated with axes labels, the title and header text. The procedure for adjusting a font is to select one of the buttons labelled "Fonts". The title, for example, is located on the "Display" property page. To adjust the font, press the button next to the text entry field that offers the current value for the title; a font dialog window appears. Then select the font parameters from the dialog window and press the "Ok" button. Once again, like the colour dialog window, this action will activate the "Apply" button on the property sheet for the tile parameters. The font will only be changed if the "Ok" or the "Apply" button is pressed.

Tile display parameters can be applied to all the tiles in a scrolled list. A property page headed "Global" allows a toggle to be set that causes the settings currently active to be transferred to all tiles when the "Apply" or "Ok" button is selected.

Two additional toggle buttons enable the transfer of ranges for the X-axis and Y-axis. It is not allows desirable to include these display parameters when the other characteristics are globally applied, but on occasion it can be useful. For example, setting the Y-axis range to that of a specific size for a set of similar spectra can provide an interesting visual effect when scrolling is used to view the data. The variation in intensity as a function of an experimental variable is highlighted in this way.