PEST1.0 - EPR - main program



This program is designed for general spectral manipulations, measurements, 
and simple calculations.  It will read all file formats.  The program is operated 
by using the arrow keys or tab keys to select an item from a menu at the top of 
the screen, and pressing the Enter key to select that item.  This manual is 
organized by menu layer and option.

1.0.1	Spectrum pages and number of data points

The default program, EPR.EXE, has room for 20 spectra of up to 2048 data 
points.  If more resolution is needed, two other programs are available:  
EPR4K.EXE has 10 pages of 4096 data points, EPR8K.EXE has 5 pages of 
8192 data points.  The simulation programs can calculate up to 4096 data 
points.

1.0.2	The screen display  ( View complete display ) 

message box
Menu-Message
The top two lines of the program data screen are called the message box.  This 
area will show the current menu selections and will post messages and prompts 
as needed.  



header box
Information
The three lines in a boxed area are called the file header area.  In the upper left 
is the current page number followed by the current filename and the file 
comment.  The next lines are status lines.
<#>		page number 	    Filename ----> Comment
SR		scan range of the current file.
FC		field center of the current file.
DP		number of data points of the current file.
XS		current X-scale factor, a multiplier applied to the display.  
		XS=1 implies no expansion.  XS=2 implies two time expansion 
		while  XS<1 implies shrinkage.
XO		current X-offset, in gauss and in number of data points.  
		XO>0 implies a shift to the right, XO<0 implies a shift 
		to the left.
Dx		distance between the two cursors measured in gauss
Dy		distance between the intersections of the current spectrum and 
		the two cursors in screen units.
p1		current data point position of the left cursor
p2		current data point position of the right cursor
Dual=		dual (overlay) spectrum page number if enabled, 
		Dual= Off if disabled.
YS		current y-scale factor, this spectrum is multiplied by this 
		number for screen display.  YS=1 -no multiplication, YS>1 
		implies a y-expansion, YS<1 implies a y-shrinkage.  The true 
		value of a data point is its screen value as measured by the 
		cursors divided by the YS factor.


display box
The large boxed area is the spectral display area.  The spectrum corresponding 
to the header above is displayed in the same color as the header print.  The dual 
(overlay) spectrum is shown in a light gray coloring if it is enabled.  Tick 
marks are arbitrary.  The dual spectrum is a copy of the original page from 
which it was obtained and changes made to the dual spectrum do not affect the 
original page.

Plot



1.0.3	Using the menus

The arrowhead (menu pointer) points to the current menu selection.
[Arrow] , [Tab]			Move the menu pointer.
[Escape] , [Backspace]		Exit from a menu. 
[ENTER]				Select that menu option. 

1.0.4	Selecting a spectral page number

[PageUp] , [PageDn] 		Select from the spectral pages.
F2 				Jump to another spectrum page.
F3				Copy the current page to another page.

1.0.5	Function Keys

The function keys are generally available whenever a menu appears in the 
message box and unavailable otherwise.  The exception is the Cursor mode 
when no menu appears and the function keys are available and in Layout mode 
when F2,F3,F4 are not available.  There are probably some others that I can't 
think of right now.

F1	Help screen will appear.  But do you really expect significant help?
F2	Jump to another spectrum page without paging.
F3	Copying the current page parameters and data to another page.
F4	Displays a list of all pages and their respective file names.
F5	Enters the cursor menu for direct manipulation of cursor positions 
	and zoom in/out of display.  These keys are then active
	[left arrow], 
	[right arrow]		Slow move the active cursor
	Ctrl-[left arrow], 
	Ctrl-[right arrow]	Fast move the active cursor
	[spacebar]		Change the active cursor
	X			Zoom the display to the region between the 
				cursors
	R			Restore the full spectrum display
F6			Toggles the screen GRID
F8			Shells out to the operating system command line.  
			Enter "exit" to return to the EPR program.

1.0.6	Moving the data display cursors

In addition to pressing F5 to enter the cursor routine, you may move the cursors 
on screen almost anytime a menu is at the top of the screen with these key 
combinations:

Ctrl-[left arrow]
Ctrl-[right arrow]	Move the current cursor to a new position.
[spacebar]		Change the active cursor
Ctrl-X			Zoom the display to the region between the cursors
Ctrl-R			Restore the full spectrum display


1.1.0	Main program options


File	Display		Calc.		Modify		Functions
HCCE	Plot		Layout		EXIT


File menu options

Load		Loads data from disk, you will be prompted for the file type.  

Save		Saves data to disk, you will be prompted for the file type.

		Binary		ASCII		Bruker		Group	


		Enter   *.*   to view a partial listing; 
		Enter   a*.*  for all the files beginning with "a".
		Enter   ...   to load multiple files at once


Directory  	Change the current directory by typing in a new path.  
		Include an asterisk  *  to view a listing of data files.

Jump		Change the display to another data page.

Copy		Copy the current data page to another data page.  You will be 
		prompted for the new page number

View		View a list of all pages with their file names.

Import		Import a file from the EPR clipboard.

Export		Export a file to the EPR clipboard

Parameters	Edit the current data parameters such as scan range, scan 
		time, etc...  View all current numeric data parameters.

Null		Replace the current data with null data.  Can apply to current 
		page or all pages.


To load more than one file of a single type, press three periods and enter at the 
file name prompt.  You will then receive a screen with prompts for entering a 
filename for each page.  To initiate the loads, go through the entire list and 
press enter at the last page.  To quit the loads, press the escape key to exit the 
list at page one.

Changing directory only modifies the current data directory and does NOT 
affect the location of the clipboard files in the  \lab\eprdata\clipfile.#  temporary 
files.

Display menu options

Scale		Changes the Y and Y scale display factors.  Does not affect 
		actual data values.
		[left arrow]	Increase the X scale
		X		Enter a specific X scale factor
		[right arrow]	Decrease the X scale
		Y		Enter a specific  Y scale factor
		-		Hold down the control key and press the 
				arrow keys for faster X scale changes
				Increase the Y scale
				Decrease the Y scale

Position	Changes the X and Y display positions.  Does not affect 
		actual data values.
			Move the spectral display left	
		X		Enter a specific X offset in Gauss
			Move the spectral display right	
		-		Hold down the control key and press the 
				arrow keys for faster X position changes
				Move the spectrum up
				Move the spectrum down

Combine		Addition or subtraction of two data sets.  If the dual 
		display is enabled, you will be prompted for the 
		Y-multiplication factors for the current main and dual 
		displays.  If the dual display is not enabled, you will be 
		prompted for the page numbers and Y-multiplication factors.  
		When completed, you will be prompted for the page number 
		to store the result.  If you do not want to store the result, 
		press the escape key.

Reset		Creates a full screen display of the current data.

Invert		Multiply the data by negative one.  Displays the results.

Dual_ON/OFF	Creates a spectral overlay for comparisons.  You will be 
		prompted for the page number of the overlay display.

Modify_Dual 	Choose to allow display modifications to either both the Main 
		and Dual spectral displays or only the Main spectrum display.  
		You will be prompted for the action.

Split		This function is for modifying the display of data collected 
		from two sources concurrently.
	Create		Combine two independent pages into one split data set.
	Separate	Separate a split data set into two independent pages.
	Kill		Gets rid of the second (lower display) data set and 
			leaves the first data set.
	Modify		Changes the relative display factors of the two data sets.

Calc. menu options 

Baseline	Corrects the data for a sloping or offset baseline.
	Linear		Fits a linear line to the ends of the chosen range
	Left		Adjusts left end of the chosen range to zero.
	Right		Adjusts right end of the chosen range to zero.
	Average		Adjusts the average of the chosen ends to zero.

		You will be prompted to apply the correction based on the 
		(1) spectral end points , or 
		(2) the spectral intersections with the two on-screen cursors.  
		The correction applies to the entire spectrum.  
		Also, you can use a low frequency filter of the 
		FT spectrum, see the Ftepr.exe program documentation, 
		to filter out many non-linear baseline effects.

Deriv		Calculates a Savitsky-Golay derivative.  You will be 
		prompted for the derivative width in points.  The greater 
		the number of points, the less resolution obtained in the 
		derivative spectrum.

Int_range	Integrates over the range between the cursors and reports 
		the sums and differences.  Can be repeated for double 
		or triple integrals.  You will be prompted for a linear 
		baseline correction based on the spectral intersections 
		with the two on-screen cursors.

Integrate	Create an integrated spectrum.

Filter		Creates a Savitsky-Golay filtered spectrum.  You will be 
		prompted for the filter width in points.  The greater the 
		number of points, the more severe the filter.

G-values	Calculates the g-values at the cursor positions.  Check the 
		scan range, field center, and microwave frequency values 
		(using the Parameters routine) to ensure g-value accuracy.

Max_min		Reports the high and low points (for the range between the 
		cursors) with point number, field value, g-value, and intensity.

Peaks		Reports all peak positions (for the entire spectral range) with 
		point number, field value, g-value, and intensity.

Modify menu options 

Baseline	Baseline corrections.  See the Calc. option documentation.

Center		Process to adjust the spectral data to be centered in the 
		storage array. This is especially useful for simulating 
		spectra since the simulation g-shift can then be set to 
		zero.  The spectrum is centered by comparing the left and 
		negative right halves of the spectrum, the 'mirror' process.  
		The spectrum display should already be adjusted so that the 
		spectral center is very near the display center.  The 
		program will iterate across a range of possible centers, 
		saving the best.  You will prompted for the final center 
		array position where the default is the computer-found 
		best center.  You may elect to keep or throw away the 
		new centered data.

Mirror		Replaces the right half of the spectrum with the negative of 
		the left half of the spectrum.

Normalize	Adjusts the total spectral intensity to 1000.0, adjusts the 
		display y-scale to 1.0.

Delete 		Replaces the area between the cursors with a linear fit based 
		on the two cursor intersections. 

Zero_fill 	Replace the region between the cursors with zeros.  

Zoom_scan 	Expand permanently the data between the cursors.  Data 
		outside the cursors will be discarded!  The number of 
		data points will not change.  For example, to permanently 
		change a 60 G scan to 40 G.

Reduce		Reduces the number of data points by a factor of one half.  
		Repeatable until 64 data points.

Splice		Increases the number of data points by a factor of two.  
		Repeatable until 2048 data points.

Functions menu options

Y-mult		Multiply the data.  You will be prompted for the multiplier.  
		The max. and min. spectral values are printed.

Y-add		Add to  the data.  You will be prompted for the constant.  
		The max. and min. spectral values are printed.

ABS		Calculate the absolute value of the current data.

Log		Calculate the natural logarithm of the current data.  
		All data values less than 1.0 will be set equal to 
		1.0 so that the minimum of the result spectrum will be 0.0.

Fit_1st		A linear fit is calculated for the data between the 
		cursors.  The intercept (b0), slope (b2), and correlation 
		(r) are displayed.

Noise		Random noise is added to the spectrum.

R-value		Spearman's Rank Correlation Coefficient is calculated 
		for two spectra.  You are prompted for the two page numbers.

Ratios		Fit the ratios of up to six component spectra to a reference 
		spectra.  All spectra must first be loaded into separate pages.  
		You are prompted for the reference spectrum page number, the 
		number of components, and the page numbers of the components.  
		The computer then fits the ratios of the components to the 
		reference and displays the results in four iterations.  The 
		maximum and minimum component ratios are 101 and 1.

HCCE menu options

Hyperfine Coupling Constant Extraction (see references).  
These routines are designed to identify and remove the spectral effect 
of an isotropic coupling constant.  

Search		Generate a 'search' spectrum where possible splittings are 
		shown as minima and the coupling value is measured from the 
		start of the spectrum.  Enter the spin value and the hyperfine 
		range of couplings over which to search.

Separate	Remove the effect of a splitting from a spectrum. Enter
		the spin value and the hyperfine range of couplings at 
		which to separate.  Each separated spectrum result will 
		appear on screen with a prompt to save the result or continue.

Minima		Sorts and prints the list of minima from a search spectrum.

Power		Raises the data in a search spectrum to a power to improve 
		resolution of the minima.

Wings		Zero the data, usually a baseline, outside the current 
		cursor positions.  This effect will reduce the noise in 
		successive separations.

Info.		Simple information about the HCCE procedure.


Layout menu options

This option has the purpose of allowing several spectra to be 
displayed and plotted concurrently and allows for extensive modification of 
combined display.  Layout has its own X,Y scale and translation values as well 
as X,Y spectral separation values which apply to all spectra in the layout.  
These values are in addition to each spectral page display parameters.  
Changing the layout display parameters does not affect the individual spectral 
page display parameters. The Y offset and separation parameters have units of 
1/10 the screen display as indicated by the vertical tick marks.  The X offset 
and separation parameters have units of Gauss.  Layout page numbers and 
display parameters are preserved even when you leave and re-enter the layout 
routine so that display changes can be made to individual pages during the 
layout process without repeating all the layout steps.

Modify		Change the current layout display modifications.  Enter new 
		values to adjust the display satisfactorily.

Add_pages	Add spectral pages to the layout display.  Enter each page 
		individually.  You may not enter a page twice.

Clear		Eliminate all layout pages and reset display values.

Plot		Enter the plot routine to output the layout display.


Plot menu options

Enables output to a dot matrix printer, an HP7475A plotter or to an HPGL 
instructions file.  For a plotter, the serial communications port interface 
values are fixed to 9600 baud, 8 data bits, 1 stop bit, and no parity; adjust 
the serial port of your plotter to these values.  The plotter should be set to 
mode A3 (US units, 11x17 inches) of the 7475A.  A null modem with hardware 
handshaking implemented should be connected between the computer and the plotter.  
See your plotter's manual for cable wiring instructions.  The following sub-menu 
items are available.

Setup		These parameters control the appearance of the plot.  The 
		default plot is the spectrum only on 8.5x11" paper.  These 
		values are reset only when the program is loaded.

Com_port	Choose the serial port number, 1 to 4.  

File		The HPGL file is ASCII text and may be transferred to many 
		different computers for output to an HPGL compatible plotter 
		or may be imported into a presentation graphics software 
		package for annotation and output to a laser printer.

Plotter		Plots to an HPGL plotter through the computer's serial port.

File		Plots to an HPGL instructions file.  This file may be output to 
		an HPGL plotter or HPGL capable printer, or may be loaded into 
		any of a number of graphics or word-processing programs that 
		import HPGL.  You will be prompted for the filename.

Print		Changes the display to white on black for printing to a dot 
		matrix printer.  The screen will be re drawn in black on white 
		for printing or screen capture.  Now press the Shift-PrintScreen 
		key combination for output through the computer's parallel port 
		to a dot-matrix printer.  Under Microsoft Windows, press 
		PrintScreen only to copy the screen image to the Windows 
		clipboard, then Paste the image into any Windows application.    
		You have two options:
	Screen		uses the current display setup including header.
	Scan		uses the entire scan display with spectral parameters.
	

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