Using the ISO-14976 spectrum viewer applet

The controls (buttons and checkboxes to the left of the window) and their use are described below, as is the html syntax required to produce the display.
 

The Controls	Mouse The system mouse may be used actively in the applet window: simply click anywhere in the window to provide a "marker" (a vertical red line), which also forms one limit of a "region of interest". The point at which the marker cuts the spectrum (x and y values) is shown in the applet "status" line at the foot of the window. Clicking and holding the mouse button (the left button, if you have more than one) while dragging the mouse brings up a second marker which forms the other limit of the region, or which can be used as an active cursor to examine the spectrum, since the read-out values remain "live" during a drag.  Buttons "Zoom in" and "Find Peak" are used in conjunction with the mouse. Click and hold the (left) mouse button at any point in the spectrum and drag (left or right) to define a "region of interest". Clicking on "Zoom in" expands the x-axis range defined by the markers to fill the available space in the whole window. "Find Peak" shows, by drawing a green line on the display, the "peak" value within the defined "region of interest". Note that the routine simply finds and records the "highest" value within the range: no curve fitting or other smoothing is applied, so the value found could be affected by noise. Note also that the routine will happily find a minimum value (an "upside-down" peak!) if the limits of the mouse defined region are both higher than the central section. CAUTION! You MUST define a "region of interest" BEFORE you click "Zoom in" "Find Peak" or "undo" for the FIRST TIME, or else the applet will "hang". Once a region has been defined, the applet will continue to function even if asked to find a peak or to zoom in without defining a fresh (current) region, but the results might be strange!   Clicking the "show All" button (at any time) forces the applet to display all the data in the decoded file, normalising intensity to "full scale" for the largest peak. This can be regarded as a "reset" button. The "Expand y" button simply multiplies the displayed y-values by a factor of 2 for each click. Peaks are allowed to go off scale and baseline values are not subtracted, so that if used repeatedly, eventually the whole spectrum can disappear! The original data are not affected, however, and may be restored with the "show All" button. "undo" has a composite function, providing one level of undo for the x-axis expansion, but also a stepwise undo for all y-axis amplification. The x-axis undo is actually a "toggle" function, the first click provides an undo, the second a "redo". This has potential for confusion if both x and y scaling are in force when the button is pressed, since two things may occur at the same time, but a little practice should soon resolve this, or alternatively once again, use the "show All" button. Finally, the "Load File" button enables the applet to display any further files whose web address (URL) may be known, and to which the current system configuration grants access permission. In the case of the example applet above, this should include the site's present directory (the one from which the applet and this file came) and its subdirectories: for convenience spectra are stored in a subdirectory called "data". Names of available spectra (contained in the "data" directory) are shown alongside the applet. Type one of these names as shown in full into the box labelled "Enter the filename" which appears when the "Load File" button is pressed, and click "OK" Any valid (fully qualified) URL pointing to an ISO-format file (anywhere on the Internet) should also work.    Checkboxes The "Grid" checkbox may be activated or deactivated at any time and provides a grid (adjusted to the scale of the current display) against which the position and height of peaks may be estimated by eye - a feature perhaps most useful for printout. The "Reverse" checkbox is provided for output from some older commercial data systems which insist on plotting binding energy increasing to the right (rather than the almost universally adopted convention in which kinetic energy increases left to right). Again this function can be applied or "undone" at any time. Use the spectrum in "data/LQtest.vms" to experiment with this (the spectrum as initially loaded should be reversed).  [TOP]
The applet in a web page	The html required to incorporate the java applet into a web page is entirely standard. The simplest applet call may be made like this:    <APPLET CODE="Visua4.class" WIDTH="550" HEIGHT="270">    <PARAM NAME="SOURCE_FILE" VALUE="PETtest.vms">    </APPLET> the required attributes and parameters being simply the location of the Java class files, the size of the applet window, and the name (location) of the data (spectrum) file. This applet will then take several default parameters - for example in this form it will not provide a "load file" button. The applet call made at the head of this page is only slightly more complex and illustrates more extensive formatting and parameter passing to control a number of applet functions.    <APPLET CODEBASE="http://www.acolyte.co.uk/JISO/classes" CODE="Visua4.class"    WIDTH="430" HEIGHT="270" HSPACE="50"    ALT="Java Applet for ISO-14976 XPS Spectra"    ALIGN="RIGHT">    <PARAM NAME="SOURCE_FILE" VALUE="data/PET_C1s.vms">    <PARAM NAME="WAY" VALUE="NORMAL">    <PARAM NAME="Y_VALUES" VALUE="HIDE">    <PARAM NAME="LOAD_FILE" VALUE="SHOW">    <PARAM NAME="START_X" VALUE="1200">    <PARAM NAME="END_X" VALUE="1208">    </APPLET> The parameter "WAY" refers to the direction of plotting, which may be "NORMAL" or "REVERSE" (for the reasons outlined above. The default value is, of course, "NORMAL" and this is assumed if the parameter is omitted). "Y_VALUES" relates to the labelling of the y axis. Here the default is "SHOW". The value "HIDE" can produce a tidier, less cluttered display. "LOAD_FILE" turns on or off the ability to load files other than the initially specified "SOURCE_FILE" into the window. The default is "HIDE" (i.e. disable the capability) "START_X" and "END_X" must be used as a pair and define specific numeric limits within the data for the initial display (useful if it is desired to draw attention to some feature in the spectrum or provide an immediate sight of a particular section of the data, for example for comparison purposes). Values for these parameters must be explicit, numerical and valid, or else the applet will "hang".  [TOP]
Using the applet locally	Using the applet locally is straightforward. Download a copy of the Java class files to a suitable directory on your hard disk, provide a source of data with a known URL (file name) and configure the html for the actions required, as described in the previous section. Likely difficulties involve the permissions set for the Java Virtual Machine for your web browser (since local files need to be read) but checking and adjusting "preferences" once again should provide a functional system.  [TOP]

 

• Don't forget to check out the ESCA Applications Notes which contain more "normal" spectra!

 

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