Changeset 520

Timestamp:

Dec 4, 2009 5:07:32 PM (14 years ago)

Author:

toby

Message:

# on 2002/01/22 21:02:55, toby did:
l-s in BKGEDT & support for functions 1-6
export to grace
cycle with "N"

File:

• trunk/doc/liveplot.html (modified) (12 diffs, 3 props)

trunk/doc/liveplot.html

@@ -79 +79 @@
 <H3>BKGEDIT</H3>
 <IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
-For most refinements, it is possible to simply select a background 
+BKGEDIT is used to fit a background function to a set of points
+selected by the user.
+For most refinements, this is not needed, 
+as it is possible to simply select a background 
 function (I find that the type 1 function, 
-shifted Chebyschev polynomials, work well)
+shifted Chebyschev polynomials, works well)
 and then refine, adding terms until a good fit is obtained.
 On occasion, poor initial fits are obtained in this manner. This is
@@ -99 +102 @@
 is good enough for the initial stages of refinement and that can be 
 refined once the model is adequate for the task.
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
+BKGEDIT can be used to fit GSAS background functions 1-6 (though
+for most purposes only type 1 is needed.)
 <P>
 <IMG SRC="b1.gif" align=TEXTOP alt="BKGEDIT screen image">
@@ -125 +131 @@
 <DL><DL>
 Note that it is advisable to place many background points in areas where
-the background varies greatly.
+the background is changing rapidly (where the background is most bumpy).
 </DL></DL>
 As background points are entered, they are saved in a file named 
@@ -138 +144 @@
 "Background points" area.
 <LI>After enough background points have been entered, the 
-"Start Fit" button turns from gray to black. When pressed, the Chebyschev 
-polynomial is fitted and the resulting curve is shown as a blue dashed line.
-<DL><DL>
-It is suggested that you start with relatively few 
+"Fit" button turns from gray to black. When pressed, the selected 
+background function is fitted 
+and the resulting curve is shown as a blue dashed line.
+<DL><DL>
+<LI>It is suggested that you start with relatively few 
 terms and add terms and background points as needed.
-Note that the maximum number of Chebyschev terms increases as 
+Note that the maximum number of increases as 
 more background points are entered.
-</DL></DL>
-The "Improve Fit" button is black when the fit did not
-converge or the number of terms has been changed. "Improve Fit" causes the
-fit to be refined starting from the previous values.
-<LI>Editing the Chebyschev terms is possible. The curve is reevaluated as 
+<LI>Editing the terms manually is possible. The curve is reevaluated as 
 changes are made.
+<LI>For the type 3 background function (radial distribution function), 
+the R terms are listed separately from the other
+background terms. These R (radii) values must be entered manually and 
+are not refined.
+</DL></DL>
 <LI>Once a good background function is determined, it can be saved in the
 experiment file by pressing the "Save in EXP file & Exit" button. This will
-set the background type to 1, and save the Chebyschev terms. 
+set the background type, and save the terms. 
 It will also turn off
 the background refinement flag for the appropriate histogram so that the 
@@ -203 +211 @@
 from the correct values of 0.042 and 3.0, respectively, to misleading 
 values of 0.036 and 0.8, 
-respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045; 
-FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036.]
+respectively. [As expected, the R(F<sup>2</sup>) stayed constant at 0.045
+with the different fixed background errors; 
+FYI, refining the background caused R(F<sup>2</sup>) to drop to 0.036, 
+so I would consider the refined background to be better.]
 <P>
 If the background is so truly irregular that only use of fixed background 
@@ -211 +221 @@
 The file used by BKGEDIT to save these points, 
 <I>EXPNAM</I><tt>.bkg</tt><I>N</I>,
-can be read into EXPEDT by typing "@R" at the initial prompt
-in EXPEDT:
+will define the background points if read directly into EXPEDT 
+by typing "@R" at the initial prompt in EXPEDT:
 <PRE>
    Is this the file you wish to use? (<?>,D,K,Q,R,Y) ><u>@r</u>
@@ -220 +230 @@
    Enter the name of your macro file: <u>GARNET.bkg1</u>
 </PRE>
-And this will enter the background points entered into BKGEDIT as GSAS
-fixed background points. If you do this you do not want to fit and enter
-Note that you are allowed to use both fixed and a refined background together,
-though this is seldom done.
+Doing this will cause the background points you entered into BKGEDIT to 
+be used in GSAS
+fixed background points. If you do this you do not want to save the 
+fitted background function as well, as this would effectively subtract 
+double the desired background.
+Note that GSAS allows simultaneous use of 
+both fixed and a refined background;
+this is seldom done.
 
 <hr><h2>LIVEPLOT/BKGEDIT Features</h2>
+<B>Plot contents:</B>
+Reflection markers can be placed using the File/Tickmarks menu item
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">or by pressing the
+"1" key for phase 1, "2" for phase 2,... Note that many attributes 
+for reflection markers can be edited using 
+Options/<a href="#configTick">Configure Tickmarks</a>
+
+<P>
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
+If more than one histogram is available to plot, it is possible to cycle 
+between the histograms by pressing the "n" or "N" (for next) key.
+<P>
 <a name="zoom"></a>
-<B>Plot zooming</B>
+<B>Plot zooming:</B>
 When the left (usual) mouse button is pressed, this defines one corner
 of a region to be magnified, as is shown to the right. 
@@ -248 +274 @@
 the mouse, but to zoom out beyond the manual zoom limits, the "reset" button
 on the manual zoom menu must be used.
-<P>
-<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
-If more than one histogram is available to plot, it is possible to cycle 
-between the histograms by pressing the "n" or "N" (for next) key.
 <P>
 <br clear=all>
@@ -292 +314 @@
 
 <img SRC="lind1.gif" align=LEFT alt="LIVEPLOT Screen snapshot">
-<P>
+
 <br clear=all>
+<P>
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+<B>Export plot to Grace</B>
+The plot can be exported to 
+<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
+that produces publication-quality graphics. Many UNIX users know 
+this program under a previous name, xmgr.
+The export is implemented 
+by producing an ASCII file with instructions that 
+creates a plot with similar formatting to what appears on the 
+screen in LIVEPLOT/BKGEDIT. However, the output quality from 
+Grace is much higher quality. Further, Grace
+can be used to enhanced and annotate the plot further.
 
 <hr><h2>LIVEPLOT/BKGEDIT Menu Contents</h2>
@@ -302 +337 @@
 <DT>Tickmarks
 <DD>Checkbuttons are provided for each phase to determine if tick marks
-are shown. See the Options/"Configure Tickmarks"menu item for information
-on tickmarks
+will be shown. 
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">Tickmarks can also be 
+toggled by pressing the
+"1" key for phase 1, "2" for phase 2,...
+Also see the Options/<a href="#configTick">Configure Tickmarks</a>
+menu item for information
+on tickmarks.
 <DT>Histogram
 <DD>This allows a histogram to be selected to be loaded
@@ -314 +354 @@
 <DD>The causes LIVEPLOT to read read the current histogram again from 
 the datafile
-<DT>Make PostScript
-<DD>Creates a low quality PostScript file containing the LIVEPLOT 
+<DT>Export Plot
+<DD>This offers options for exporting the plot in multiple formats.
+I am hoping to add more export formats eventually.
+<DL><DL>
+<DT>to PostScript
+<DD>Creates a <I>low quality</I> PostScript file containing the LIVEPLOT 
 output. See the Options/"Set PS output" button for where the file is created.
+Most unix systems are capable or printing PostScript files.
+On Windows, a program such ghostview may be needed to translate the 
+PostScript to a format that can be viewed or printed.
+<A name="grace">
+<DT>to Grace
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36>
+<DD>Plots can be exported to 
+<A HREF="http://www.nist.gov/cgi-bin/exit_nist.cgi?url=http://plasma-gate.weizmann.ac.il/Grace/">Grace</A>, WYSIWYG 2D plotting tool for X-Windows
+that produces publication-quality graphics. 
+After the plot is exported, it can be further 
+enhanced and annotated in grace.
+</DL></DL>
 <DT>Quit
 <DD>Exits BKGEDIT/LIVEPLOT.
@@ -324 +380 @@
 <H3>Options Menu</H3>
 <DL><DL>
-<DT>Configure Tickmarks
-<DD>Tickmarks can be placed automatically, similar to their
- placement in POWPLOT or can be drawn one height to another. The default
+<a name="configTick"></a>
+<DT>Configure Tickmarks<DD>
+This submenu provides options that controls how tickmarks are displayed.
+<DL><DL>
+<DT>Auto locate<DD>
+When this option is selected, tickmarks are placed in different positions
+for each phase, automatically, similar to how tickmarks are shown in POWPLOT.
+<DT>Manual Placement<DD>
+Tickmarks are drawn at specific heights that can be set for each phase 
+(see below). The default
 is for lines to be draw from "-Inf" to "Inf", which creates lines from the
-bottom to the top of the plot. The options for each phase allow the line to be changed between solid and dashed, color of the line can be specified and 
-the vertical placement of the tickmarks can be specified. The "show" flag, 
-set in the File/Tickmarks menu can also be changed here.
+bottom to the top of the plot. 
+<DT>Label by name
+<IMG SRC="new.gif" HEIGHT=13 WIDTH=36 alt="New!">
+<DD>
+By default, a label "Phase1",... is displayed in the legend when tickmarks
+for that phase are displayed. When this button is pressed, the first 
+20 characters of each phase name (phase title) are used instead. This
+label can be edited, as described in the next paragraph.
+<DT>Phase <I>n</I> opts<DD>
+The options for each phase allow the line to be changed between 
+solid and dashed, color of the line can be specified and 
+the vertical placement of the tickmarks can be specified. The 
+"Show Reflections" flag, 
+set in the File/Tickmarks menu,
+as well as the label used for the phase can also be changed here.
+
+</DL></DL>
 <DT>Obs Symbol (Symbol Type)
 <DD>This brings up a menu where the symbol type and size for the