SPECPR Users’ Manual                                                   Page 9.1



9.1 Introduction The CRT plot routines are a set of routines for data display, overlay, header information display and change, data print-out, and specific graphics-oriented routines to read data values off of the plot and to analyze specific absorption features. The CRT plot routines are called from the completion of a Math Operation (Chapter 8) or from the File Display, Transfer and Overlay routines (Chapter 10). Any x-y paired data may be plotted. The horizontal axis may be labeled to properly describe the data; the default horizontal-axis label is "Wavelength (microns)", but the default can be overridden. Data may also be plotted as a function of channel number, or the x-axis values inverted in which case the default units of microns is assumed and the program converts the units to wavenumber in inverse centimeters. The CRT plot routines also have a facility for removing spikes or glitches in data by assuming the glitch was caused by a bad bit in the data. The user may also elect to change any channel to a deleted point.

9.2 Plotting Mode The plot mode is selected by the command letters

h    for channel,
a    for wavelength, or
n    for energy (inverse wavelength).

When you have a plot on the screen, change the plot type by entering h, a, or n and return. The menu for these commands is always located at the bottom of the plot screen. Note the characters chosen are the second letter of channel, wavelength, and energy since the first letters are used for other commands. The energy mode assumes the wavelengths are in microns, and the inverse wavelengths are computed in wavenumber.

9.3 Changing Scale The scale of the CRT plot is controlled by four values: the minimum and maximum for the horizontal ("wavelength") axis and similarly for the vertical axis. The plot scale may be changed by a command where the user types the desired limits, or by graphically selecting a window within the current window.

9.3.1 Changing Scale by Typing in the Range The scale is changed by typing the


command. You are then given the following menu.

 Current Scale: VERTICAL= 0.0000E+00   2.0000E+00
                HORIZ.  = Automatic

To scale the plot, type in the mode (n or w) and horizontal axis limits first.
 When the vertical scale is entered, the routine will exit to the plot.

 type  n  and left and right hand limits for INVERSE WAVELENGTH, or:
 type  w  and left and right hand WAVELENGTH limits
          (if you type  w  only,  the program will AUTOSCALE the limits
          from the current wavelength set)

 Type lower bound and upper bound values for the VERTICAL AXIS, or:
 type  A  to AUTO SCALE (the VERTICAL AXIS), or:

In order to change the horizontal axis range, you MUST change its range before the vertical axis. As soon as the vertical axis range has been changed, the routine automatically exits and the plot is redone. For example, to change the scale from 0.0 to 1.1 from the CRT plot, type

            0 1.2

command sequence. If you wish to change the horizontal scale to 0.2 to 3.0 and the vertical scale to 0.5 to 1.3, type the

            w.2 3
            0.5 3

command sequence. The format is completely free: there is no need to add a decimal point on integers. If you type a mistake, the routine will flag it and ask you to retype the values. Specpr allows commands to be separated by semicolons, so it is often desirable to see the plot while changing the scale. This can be done all from the CRT plot screen: enter the "c" command and the ranges separated by semicolons. Thus

c;w.2 3;0.5 3

is equivalent to the

              w.2 3
              0.5 3

command sequence. In order to autoscale the horizontal range, type a "w" command with no minimum or maximum. To autoscale the vertical range within the current horizontal range window, type an "A" command. Thus to autoscale both the horizontal and vertical ranges from the CRT plot screen, type the




command sequence.

9.3.2 Changing Scale by Graphics Sub-Window A window within the current window may be selected to change the plot scale using the graphics cursor. NOTE: this option currently only works on X-windows or Hewlett Packard compatible graphics terminals. To change the sub-window, type the


command from the CRT plot command screen. The CRT menu will be erased and a new menu written asking you to position the graphics cursor at the position on the plot where you want the upper left corner of the new sub-window. Place the graphics cursor at the correct position and press the return key. Next you will be instructed to select the lower right corner. Place the graphics cursor at the desired lower right corner and then press the return key. The CRT plot will then be rescaled to the new window. Note that you can not use this command to scale to windows larger than the current window. It is, however, a very useful command for enlarging small features on the plot.

9.4 Line Type Each data set on a CRT plot may have a specific line type. The line types available may be dependent on the terminal type, but the line type also has a few different ways of plotting the data, for example by including a small cross at the actual point on the plot. Typing the


command (the lower case letter L) followed by a number from 0 to 9 will change the line type used in the CRT plot. The following shows the characteristics of line types on HP series graphics terminals.

        Line             Description
         0      error bars included, crosses, not connected (+ + +)
         1      error bars included, crosses, connected (+—+—+)
         2      error bars excluded, points connected ( ———— )
         3      only small error bars excluded, points connected ( ———— )
         4      error bars excluded,  line: — - — - —
         5      error bars excluded,  line: ——— ——— ———
         6      error bars excluded,  line: ——  ——  ——
         7      error bars excluded,  line: ...........
         8      error bars excluded,  line: —— - —— - —— -
         9      error bars excluded,  line: --- --- ---

9.5 Horizontal Axis Labels The default axis label for the specpr CRT plot is "Wavelength (microns)", but this label can be changed. The change is done in the wavelength set by changing line 4 of the manual history. For example, say you had a data set of intensity versus time, and the time data set was in seconds. Change line 4 of the manual history to read "\\W Time (seconds)" (no quotes in the manual history), and the CRT plot horizontal axis label will read "Time (seconds)". The key sequence for axis labels is the \\W (the backslash is important).

9.6 Changing the Wavelength Set The wavelength set contains the "x-axis values" which make the plot of x-y paired data possible. The number of channels plotted is also controlled by the wavelength set in use. For Math operations, the number of channels that are written to the data file is controlled by the wavelength set in use AT THE TIME THE USER EXITS THE CRT PLOT ROUTINES. A different wavelength set can be selected by entering the upper-case file-ID-letter and the record number. For example:


selects file "v", data set record 234 as the current wavelength set. You may also assign channel numbers to the "wavelength set" by typing a "C" and the number of channels. For example:


sets channel 1 to be "wavelength" 1.0, channel 2 to be 2.0, and so on to channel 2314 which is set to 2314.0.

9.7 Graphics Cursor Position

WARNING: the graphics cursor read routine currently only works with X-windows or HP-compatible graphics terminals. Often you want to know a particular data value that is displayed on a plot. The graphics cursor read routine allows you to place the cursor on a particular data point, press return, and the closest channel number, wavelength, and data value are displayed, along with the equivalent wavelength and data value for the cursor position on the graph. This position capability also allows you to graphically interpolate a value if you are trying to estimate a data value. To begin the graphics cursor read routine, type a


command (be certain it is upper case g, because lower case g is the glitch removal routine). Next, use the graphics cursor arrow keys on the graphics terminal to position the cursor to the desired location on the CRT plot. Then press return to get the position displayed. To exit the cursor position routine, type an





9.8 Interactive Band Analysis The interactive band analysis routine is a graphically oriented absorption band analysis system. The user selects continuum points graphically, the system then removes the continuum, and the user can select the band center or let the routine find it. The Full Width at Half Maximum (FWHM) works similarly. The routine can write the results in ascii to a user selected file. WARNING: this routine currently ONLY works with X-windows or Hewlett-Packard compatible graphics terminals. The routine is entered from the CRT plot routines by typing an


command. The routine then prompts the user for one of three actions: the changing of the vertical and horizontal scales, the opening of a new file, or the analysis of a band. The changing of the plot scales is by a


command. The scale change command calls the plot scale routine, so it proceeds exactly as the normal scale changing is done in plotting a spectrum (see section 9.3). If the user wishes to open a new output file for writing the ascii results of the analysis, type an


command. You will then be prompted for the file name and a title for the data which is to be written. The "automated, interactive band analysis" is started by issuing an


command. You are first prompted for the first point which lies on the continuum which surrounds the band of interest. After this prompt is given, you are expected to use the graphics cursor position keys to move the cursor to the first continuum point and then to enter a return. A box is then drawn around the nearest channel in the data set (i.e. the continuum points can be selected by locating their proper horizontal position alone and ignoring the current vertical position of the graphics cursor). After the first point has been selected you are then asked whether this point is at the right position, if it is not, you may redo it by typing an


or you may continue by entering a return. Once you have selected the first continuum point, the process is then repeated for the second continuum point. If both points are correct you enter a return and the data are scaled by dividing out the continuum and then the continuum-removed spectrum is plotted. At this point in the analysis you must determine whether you would like to move the locations of the continuum points (command "m"), change the plot scales (command "c") or have the band center selected (return). If you decide to do another continuum the new one is done using the same process by which the original continuum was selected. The only exception is that the data for the y axis which is used to select the new continuum is no longer the original data but is instead the continuum-removed spectrum currently displayed on the screen. If you wish to rescale the data, it is done in the same manner as in the normal spectrum plotting routine. If you decide that all is correct and the band center should now be selected, the program begins its analysis with a return command. The program first searches the continuum-removed data to find the minimum channel between the two selected continuum points. Once the minimum point has been found, a parabola is fit to the minimum point and the two points nearest to this minimum. The center wavelength (x-coordinate) of this parabola is then calculated as well as the reflectance (y-coordinate) on the parabola at this point. A solid vertical line is then plotted from this calculated set of coordinates to the continuum. The reflectance level of the Full Width Half Max (FWHM) is then calculated and the FWHM is then itself drawn as a dashed line between the sides of the band with its endpoints being solid boxes. A vertical dashed line at the mid-point of the FWHM is then drawn from the reflectance level of the absorption feature to the continuum. If there are enough channels (10 channels are currently being used as the limit) between the two end-points of the FWHM the routine will draw a cross at the Full Width Quarter Max (FWQM). This routine repeats this process determining whether it is possible to find the subsequent full widths (e.g. Full Width Eighth Max) by examining the number of channels as determined by the previous full width. The last full width that can be determined is the Full Width Sixty-fourth Max. The last FWQM (if present) or subsequent width which has been located is drawn as a dotted line with its endpoints being two small solid boxes. The center of this width is then computed and a vertical dotted line is draw from its intersection with the data to the continuum. You are now asked whether you would prefer to use the fit selected center (return) or to manually select the band center by an


command. If the fit selected center is chosen the FWHM is calculated, as well as the asymmetry parameter and the band depth with the band center and FWHM being written to the terminal. If you choose to manually select the band center you must manually move the graphics cursor (as before) to the correct horizontal position. A Full Width Half Max is then drawn on the graphics screen and is calculated and then written to the terminal. After the band center has been selected you have the option to redo the center with an


command, or to venture forward (return). Next, you have the option to select the FWHM manually with an


command, or to have the width selected automatically. If manual selection is chosen, a horizontal line is drawn at the proper reflectance level and you then select two points on that line in a manner similar to chosing the original continuum (Note: with noisy data, manual selection may need to be used). After the FWHM has been determined by either of the methods above, you are then asked whether the error associated with the horizontal data should be determined automatically (return) or picked by the user with an


command. The automatic error selection finds the first two points on either side of the channel nearest the band center and takes their absolute difference divided by four as the horizontal error value. If you wish to determine the horizontal error manually, you enter two points in a fashion similar to the selection of the continuum or the manual determination of the FWHM. Once the error has been obtained by either method, you are asked whether the data should be written to an ascii text file (default). If you choose not to write the data to a file with an


command, the routine then asks if you would like to exit (command e) or begin the entire process again (return). If, however, you wish to write the data, the program prompts you for a file and title for the data if a file is not currently open. You then receive a prompt for a 15 character comment (longer comments are silently truncated) which describes the band (you may wish to standardize the content of this field when analyzing many bands). After a comment has been entered the program asks you if you want to exit with an


command or to begin the entire process once more.

Known crashes: 1) If one attempts to run the program to analyze a band with a large number of deleted channels, the routine seems to get confused and crashes specpr.

9.9 Deleting Individual Data Channels Individual data channels may be marked as deleted by typing the


command followed by a list of channel numbers followed by a


command. Internal to specpr, the deletion is done by setting the value of the data in the specified channels to -1.23×1034. Thus, once a data point has been deleted, its value has been changed and it can’t be undeleted. The list of channel numbers consists of numbers separated by spaces and by pairs of numbers separated by a "t" (meaning to or through). For example:

r 1 2 55t63 77 117 t 120 c

means to delete channels 1, 2, 55, 56, 57, 58, 59, 60, 61, 62, 63, 77, 117, 118, 119, and 120. If you forget the "c", the routine will ask for another line of deleted points until a c, for complete, continue, is entered.

9.10 Glitch Removal Typing


from the CRT plot will call the glitch removal routine. The routine tries to identify glitches by looking for data points which are greater than 6 percent of the total data range and, by the use of a simple pattern recognition routine, checks 4 conditions. The data points which are thought to be glitches are identified by a small diamond shaped symbol. The user can then select which data points are "actual" glitches and can then correct them. The glitches are assumed to be wrong by some power of 2 from the true data. This follows from a binary counter where one of the bits has been set wrong. This routine was written specifically for the University of Hawaii "Wedge" CVF spectrometer which has these type of counters, but most modern digital instruments are similar and this routine may work for them. WARNING: once the data have been multiplied or divided, the glitch removal is an estimate of the actual data and thus strictly speaking, is "fudging" the data. The user indicates which channels are to be "deglitched" by selecting all data points marked on the graph, only those indicated by a list, or all those selected by the program except for those in a list. By typing an


command, the user tells the program that ALL the points identified plus the channels typed in after the "a" are glitches to be corrected. By typing an


command, the user tells the program ONLY those channels typed in after the letter "o" are to be corrected as glitches. By typing the


command, all the channels identified by the program are glitches BUT those channels which are typed in after the "b". At least one space must occur between channel numbers. The glitch routine searches for 15 glitches at one time so it may take more than one pass to remove a lot of glitches. Sometimes more than one bit is wrong, and it will take more than one pass. Glitches which occur next to each other are not recoverable by this routine since the routine tries to correct the point to the surrounding data using the nearest power of 2. If after 2 passes on the same point the data value is not restored, it is probably lost. A note on removing glitches: you are fudging the data. If you are not very careful and use the utmost restraint, you may create some absorption or emission features you had not counted on!

9.11 Information Display and Information Change Every standard specpr data set contains extensive header information, including the title, history, dates and times of data acquisition and data processing, as well as many others. Appendix A lists the specpr format, and all the header information values may be displayed and changed in the Information Change routines. To change header information, type the


command from the CRT plot screen. The header information is contained on many pages, the first of which displays the title. Pressing return goes to the next page, and typing


from any page returns to the first page. To change information on any page, type the indicated letter. You will then be instructed to input the appropriate data. In the case of the manual history, which is displayed in 4 lines and can be changed one line at a time type


and the line number or simply the line number 1, 2, 3, or 4, or to change all four lines, type "m"and no line number. In the case of the Band Normalization factor, scan time, or total integrating time, the number can be integer, floating point, or scientific notation. In the case of scientific notation, the number is typed in as an integer or real number, then the letter e, then the exponent (to the power of 10, an integer). Thus


is equivalent to


There are 3 ways to exit the information change routine. When at the last page, pressing return with no input will exit to the CRT plot. Typing


from any page will also exit to the CRT (graph) plot. Typing


will return to the calling routine (Math Operations or File Display and Transfer). The "e" exit command will not terminate other processing; it only skips the CRT plot. Thus, if a file write is pending (as in the Math Operation, Chapter 8, or file transfer with display, Chapter 10), it will be completed in the type e exit. If you wish to exit and terminate pending file writes, type


for a hard exit. Note that, from the data display routine (Chapter 10), no information is changed on the stored data unless there is a transfer involved (see Chapter 10).

9.12 Printer Listings and Printer Plots The entire header information and data (in scientific notation) can be listed on the printer by typing the


(print data) command. The data can be plotted as a printer plot with the current vertical scale by typing


and the number of copies (10 or less). The data can be plotted in a printer plot only as a function of channel number. The vertical-axis resolution is 1 part in 100 (100 print positions for the plot). For each data point printed, the wavelength, channel number, and data number are given. Four pages are required for 256 data points and 2 pages for 120 points. When the number of channels is less than 120, the plot is scaled to fit from 1 to 2 pages.

9.13 Multiple Commands in the CRT Plot Routines One entire line (80 characters) can be input to the CRT plot routine at one time for execution. For example, to change the wavelength data set to file v, record 2, change scale, print a printer plot, and set the line type to 3, you would type the



V2 c p l3

Spaces can be inserted wherever desired but are not necessary. This multiple command capability greatly speeds up processing since it may take several seconds to plot the data on the CRT and would take a long time to replot the CRT after each command (on a standard graphics terminal; X-windows is typically only a fraction of a second).

9.14 Exiting the CRT Plot Routines There are 3 commands for exiting the CRT plot. The normal method of exiting the CRT plot routines is by typing an


command. In this case, the user soft exits from the CRT plot in the normal fashion and the program executes the next command. The "hard exit", terminate all pending commands, is the


command. With the "x" exit command, specpr returns to the calling routine (which is either Math Operations or File Display, Transfer, and Overlay). After a soft exit (e) from the CRT plot under Math Operations, the data set is written to the requested location (see section 8.7). If errors are included, the program writes on the CRT where they will be written and gives the user the option of not writing the error data set (by typing an


command). Otherwise, press return or type a


command to continue. After a soft exit from the CRT plot under File Display and Transfer, the data set is written only if there is a transfer (see Chapter 10); otherwise, the next command is executed. The third way to exit the CRT plot routines applies to the Math Operations routine only. If the Band Normalization option was not turned on, the user may type a


command. This will turn on the Band Normalization option, exit the CRT plot, and go to the Band Normalization routine (section 8.9). When the Band Normalization routine is left, the program will return to the CRT plot. If the "b" command is entered while in the file display, transfer, and overlay routines, the CRT plot will soft exit (as a type "e" exit above).