SPECPR Users’ Manual                                                   Page 13.1

CHAPTER 13

PLOT ROUTINES FOR WORK AND PUBLICATION

13.1 Introduction The specpr hardcopy plot routines are designed to provide publication quality plots for general x-y data sets. Specpr builds two intermediate files: a vector file and a text file. The files are plotter device independent. Specpr then starts a Unix daemon process that reads the files and plots the data on a specific plotter. The daemon process is device dependent. While some users have written programs to use several different plotters and even laser printers, the most commonly used plotter is an HP7550-compatible plotter. This chapter is specific to the HP-compatible plotters, but will work in general for all other plotters so far implemented. The plot routines are called from Program Operations by typing a

p

command. When you first enter the routine, the first command will list the available plotters. This may be site dependent.

13.2 Plotting Mode Type The first step in setting up a plot is to select the plot mode. Type

w

to plot in value versus wavelength,

n

to plot in value inverse wavelength. In this case, you specify a wavelength set in microns and the plot routines convert to wavenumber where wavenumber increases to the right. To plot in wavenumber, as above, but with wavenumber increasing to the left (reverse of the above mode), type an

r

command. If you want to use your own horizontal axis label, type

y

(the plot will be linear). You will then be asked to type in the horizontal axis label (24 characters). For example, you might type:

TIME (SECONDS)

or whatever your data correspond to. Thus, you may do any kind of one-dimensional array processing you wish.

13.2.1 User-selected wavelength limits If you type only a letter for the plot mode, the horizontal axis is scaled to the range covered by all the wavelength sets used in the generation of the plot. However, you may select the wavelength limits for the plot, regardless of the wavelength sets used. When you type in the "w" for wavelength mode (or n, r, or y), also type (on the same line) the minimum and maximum wavelengths for the plot. Type in wavelengths the inverse wavelength modes (n and r) also. Example:

              w 0.325        2.60
              n 0.325        2.60
              r 0.325        2.60
              y 0.325        2.60

The actual limits on the plot will be 2% greater than the range (maximum-minimum) on each side (see section 13.5 for details). The left bound is then minimum minus 2% of the maximum-minimum range, and the right bound is the maximum plus 2% of the maximum-minimum range. You can suppress the addition of the 2% by adding the option

n

after the limits. For example,

w 0.325 2.60

would produce actual limits of 0.2795 to 2.6455. However,

w 0.325 2.60n

would keep the actual limits at 0.325 and 2.60. To exit the plot routine, type an

e

or

x

command anywhere in the routine.

13.3 Vertical Axis Label Several vertical scale labels are displayed for you to select. They are numbered 1 to n, where n is currently 8. To select one of these, type in the number. If you wish to type in your own label, type the number (currently number 9) that says "type in your own label," and you will be instructed to type in a label of not more than 60 characters. If you wish to plot the vertical axis in log (base 10) of the input data, type

10

and you must type in your own vertical axis label. The program will then proceed to the Delete From All Spectra section. Type

e

or

x

to return to the beginning (section 13.1).

13.4 Delete From All Spectra If, from all the spectra you are going to plot, you wish to delete one or more channels common to all, type a

d

command. You will then be instructed to type in the channels that will be deleted from all spectra to be plotted. At least one space should be left between each pair of channels, and more than one line can be used for input. All channels may be deleted if desired. When you are through, type

c

to continue to the scale section. Type

e

or

x

to return to the beginning (section 13.1). When typing in a sequence of channels, you may give the beginning channel, a

t

and the end channel. For instance, to delete channels 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 23, and 24, you could type

d1t8 15t17 23 24c.

13.5 Scale of Plot The vertical scale of the plot is selected by the user. Type in the lower and upper bounds of the plot. The plot size is 13.5 centimeters (vertical axis) by 21.7 centimeters (horizontal axis) for the data plot area on the HP plotter. However, the plot size does vary somewhat with other plotters. If your data are to be plotted in log space on the vertical axis, the lower and upper bounds should be input as ordinary numbers. The program will convert the scale limits and data to logs. The scale is then labeled as the log of the number. Type

e

or

x

to return to the beginning of the plot routines (section 13.1); otherwise, the program will go to the Plot Scale Factors section (section 13.6).

13.6 Plot Scale Factors Next you are asked to enter the plot horizontal and vertical scaling factors. These factors must be less than 1.0 and scale the size od the data area of the plot. Thus if the original size of the plot was 17 centimeters high, a vertical scale factor of 0.5 would make it 8.5 centimeters. These scale factors do not affect the text or the text size.

13.7 Data Set Input and Options The data sets to be plotted are input as the file ID (v, w, u, y, or d), the record number, and the options. For all data sets entered, the wavelength set must be specified. If it is not, unpredictable plots can occur. A maximum of 50 spectra may be plotted at one time. These may be all on one graph or separated into many plots by an option request. The options are listed below.

Option B means to plot symbols as Black (assuming the black pen is used on HP compatible plotters), the same color as the axes labels. The default is to use the same pen color as the data.

Option c means to Connect the data points. If the wavelengths are not in sequence, or a if channel has been deleted, the points involved are not connected.

Option C means to Always Connect the data points. This option permits the wavelengths to be NOT in sequence, but will connect them anyway.

Option d means to delete points from this data set only (as opposed to delete from all data sets as in section 13.4). The program will ask for channels to be typed in when it is ready. More than one line may be used to input the channels to be deleted. When you are finished entering channels, type

c

to continue.

Option e is include Errors.

Option E is include Errors, but only when the error bars are large enough to be recognized on the plot.

Option g means the spectrum after this one is to be plotted on a new graph. Thus, 50 spectra may be plotted on a single graph (overlaid), or they may be plotted singly or any combination. The g (new Gould plot) selects when a new plot is to begin. The "g" works the same for non-Gould plotters also.

Option l followed by a number 1 through 8 selects the line color for the plot. The line color for HP-compatible plotters is the pen number. The default is size 1.

The line color for some implementations is device daemon dependent. For the Gould electrostatic plotter this number represents the line thickness. the axis is fixed at 3. The number 1, 3, 5, or 7 is the width of the line in Gould units. Size 1 is about 1/200 of an inch (0.127 mm). The line size changes error bars and the line connecting points.

Option L is the Line type. For HP-compatible plotters it varies from solid to various dot and line patterns. See Figure 13.7.1 for specific examples.

Option m More copies: In the options, specify "m" and the number of copies desired (1 to 9) default=1. Note that you need this option only on the last spectrum to be put on the plot.

Option n means that, if a point lies outside the lower or upper bound, it should be deleted. If this specification is not given, the point will be plotted at the limit of the graph.

Option o means to offset the data, followed by the amount to offset. You can use any positive or negative number. This number is added to the data before it is plotted. For example to offset data set v23 with its wavelength set v22, you could type:

v23V22o2.2

to offset by 2.2 data units.

Option p followed by a number is the point size. This number can be 0 to 5. If the number is zero, no point will be plotted. Point size 1 is about 1.27mm on a side, size 2 is twice this, size 3 is three times, etc. Note, if point size zero is specified and points are not connected, no data will be plotted, and you will have a blank plot! A line drawing can be made by specifying point size zero and connecting points. The default point size varies with the total number of channels per spectrum. It is size 3 for 30 channels or less, size 2 for 31 to 100 channels, and size 1 for more than 100 channels. The symbol type changes with each spectrum plotted. See Figure 13.7.2.

Option r Because mistakes are bound to happen when typing in all these data sets, you may return to the last step for re-entering your data. This is done by typing an "r" in place of a file ID and record number. Example: You type in the spectra

1) "v23eV2p3" 2) "v29eV2p4" 3) "v30p1c" 4) "v33V5".

You now notice the step #3 should have been "v31V3p1c". You are at step 5: you type "r"; the computer says

"RETURN TO 4; CONTINUE".

You then type "r" again, and the computer responds

"RETURN TO 3; CONTINUE".

You may then retype step 3 (and also all steps after 3). You may not return to a step before the first data set entered (if you need to, you must "e" or "x" to exit).

Option s Symbol type: To change symbol type, specify "s" and the symbol number (1 to 8). See Figure 13.7.2. The symbol size is given by the "p" specification (point symbol size). The symbol type is incremented for each spectrum input and is reset to 1 for each new plot ("g" specification).

Option t means to include text on the graph. Text may be written as 15 sets of 70 characters per set for each spectrum entered. The text position is given in centimeters [horizontal direction (x), then vertical (y)] from the lower left-hand corner of the axes of the plot. After the x and y position, input the text angle (90° is horizontal and 0° is vertical) and then the text to be added. When all text is entered, type a

c

to continue to the next data set.

Symbols may be plotted using the text mode. Instead of x, y, degrees, text, you enter

s <symbol type> <size> x y

where <symbol type> is the symbol described under the "s" option. The symbol size is also described under the "s" option.

Terminate entry of the text mode and continue entering data sets by typing a

c

command.

Option V, W, D, U or Y followed by a record number sets the wavelength set to be used (the horizontal axis values).

Notes on Text entry: You may also return to the previous text entry using the "r" specification as with the data set input. You may not return to a previous entry before text entry 1. If you have an error in a previous file entry, type "c" to continue to next step after text entry; then return to the last data set input as described above. The specpr plot routines allow subscripting, superscripting, backspacing and greek and math characters in the text. Special characters are used to enter the different modes and can be used wherever text is written on the plot (horizontal or vertical axis labels or other text). The characters are:

Character Effect
\ (Backslash) Backspace to previous character
\{ (Left Brace) Go into subscript mode
} (Right Brace) Go into superscript mode
@ (At sign) End last scripting mode
! (Exclamation Point) Toggle greek/normal mode (see table 13.7.1)
| (Vertical Bar) Toggle math/normal mode (see table 13.7.2)

NOTE: the \\ is necessary before "{" because these brackets are used by
the command interpreter for variable parsing (section 2.6). The "\"
escapes the "{" so that it is not interpreted by the command line
variable parser.

   Table 13.7.1

Greek character set
--------------------
Α α  A a    Ν ν  N n
Β β  B b    Ξ ξ  C c
Γ γ  G g    Ο ο  O o
Δ δ  D d    Π π  P p
Ε ε  E e    Ρ ρ  R r
Ζ ζ  Z z    Σ σ  S s
Η η  Y y    Τ τ  T t
Θ θ  H h    Υ υ  U u
Ι ι  I i    Φ φ  F f
Κ κ  K k    Χ χ  X x
Λ λ  L l    Ω ω  W w
Μ μ  M m
--------------------

Example: 1.04μm would be entered as:

1.04!m!m

                             Table 13.7.2

                         Mathematical Symbols
      --------------------------------------------------------------
      A   infinity (∞)                   _     _
      B   improper superset (⊇)          a   ⇑
      C   proportional (∝)               b   ↓
      D   union (∪)                      c   section (§)
      E   root extender (‾)              d   @
      F   bell ()                       e   double dagger (‡)
      G   plus or minus (±)              f   |
      H   less than or equal to (≤)      g   improper subset (⊆)
      I   greater than or equal to (≥)   h   \\
      J   square root (√)                i   circle (◯)
      K   terminal sigma (ς)             j   partial derivative (∂)
      L   integral sign (∫)              k   empty set (∅)
      M   subset (⊂)                     l   {
      N   superset (⊃)                   m   }
      O   intersection (∩)               /   /
      P   not (¬)                        "   "
      Q   clover leaf (¢)                #   #
      R   angstrom (°)                   ’   ’
      S   gradient (∇)                   +   +
      T   times (×)                      -   -
      U   divide (÷)                     *   *
      V   identically equal (≡)          <   <
      W   approximately equal (≈)        =   =
      X   not equal (≠)                  >   >
      Y   ←                              ^   ^
      Z   →                              ‘   ‘
      --------------------------------------------------------------

It was assumed that these characters would not need to be printed so they have been reserved for the above special use. Backslash can be used to cause characters to be overprinted. An "@" (at sign) terminates the last use of a brace. All characters in between are printed in script mode.

Examples:

                      A\{1@  Will print as A1

                     SAM\\\___    Will print as ___

X}2@-Y Will print as X2 - Y

Typing

e
or
x

in place of a file ID will cause the program to return to the beginning
of the routine (section 13.1).

Typing

b

will begin building the vector and text files
on the disc. As soon as these files are complete, specpr starts the
plot daemon job and returns for more input. Thus while the plotter
is plotting, you may do other tasks, including creating more
plots.