Changeset 1181

Timestamp:

Nov 25, 2011 4:15:38 PM (9 years ago)

Author:

toby

Message:

move Topas-able liveplot to stable release

Location:

trunk

Files:

• doc/liveplot.html (modified) (2 diffs)
• liveplot (modified) (13 diffs)

trunk/doc/liveplot.html

@@ -51 +51 @@
 Some of the features available in LIVEPLOT are:
 <UL>
-<LI><IMG SRC="new.gif" alt="New!"> 
+<LI><IMG SRC="new.gif" alt="New!">
+  Plotting of Topas refinement results in LIVEPLOT:
+  Upon request, LIVEPLOT has been augmented to read in results from
+  Topas, as well as GENLES.
+  <a HREF="#Topas">See below for details.</a>
+<LI><IMG SRC="new.gif" alt="New!">  
 Regions of the plot can be magnified to show more detail, for example
   in regions at high Q. 
@@ -432 +437 @@
   
 </UL>
+<a name="Topas"></a>
+<B>Plotting of Topas refinement results in LIVEPLOT</B>
+Upon request, LIVEPLOT has been augmented to read in results from
+Topas. Follow the procedure
+<A
+  HREF="http://topas.dur.ac.uk/topaswiki/doku.php?id=outputting_publication_quality_plots_using_expgui">Publication
+  Quality Plots using Liveplot in EXPGUI</A> from the <A
+  HREF="http://topas.dur.ac.uk/topaswiki">Durham University Topas Wiki</A> to
+  generate an output file that LIVEPLOT can read. Then use the "Import
+from Topas" menu item in the File menu to open a dialog window where
+the file can be imported. It is optimal to use the extension
+<tt>.ascii</tt> for the Topas export file.
+<P>
+Note that in normal use, LIVEPLOT is started from inside EXPGUI with
+an open .EXP file. If LIVEPLOT will be used frequently for Topas, it
+may be useful to create a shortcut to start LIVEPLOT directly. This
+can be done in Windows by following these 
+<A
+HREF="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/InstallWindows#shortcut">instructions
+to make a short cut</A>, but reference file <tt>.../expgui/liveplot</tt>
+rather than file <tt>.../expgui/expgui</tt>. Similar things can be
+done in Linux and on the Mac. 
 
 <hr><h2>LIVEPLOT/BKGEDIT Keyboard Shortcuts</h2>

trunk/liveplot

@@ -15 +15 @@
 set exitstat 0
 set expnam [file root [lindex $argv 0]]
-if {$expnam == ""} {catch {puts "error -- no experiment name"}; set exitstat 1}
+#if {$expnam == ""} {catch {puts "error -- no experiment name"}; set exitstat 1}
 if $exitstat {
     catch {puts "usage: $argv0 expnam \[hist #\] \[legend\]"}
@@ -107 +107 @@
 }
 set expgui(RadiiList) {}
+set ::expmap(phaselist) {}
 
 proc waitmsg {message} {
@@ -252 +253 @@
     global expgui modtime expnam
     if [catch {
-        set modtime [file mtime $expnam.EXP]
         set loadtime [time {
-            if {$expgui(tcldump) == ""} {
+        set modtime 0
+            if {$::topasfile != ""} {
+                set p "TOPAS import"
+                readdata_topas $box
+            } elseif {$expgui(tcldump) == ""} {
+                set modtime [file mtime $expnam.EXP]
                 set p HSTDMP
                 readdata_hst $box
             } else {
+                set modtime [file mtime $expnam.EXP]
                 set p TCLDUMP
                 readdata_tcl $box
@@ -357 +363 @@
     calcvec set $calclist
     bckvec set $bcklist
-    diffvec set [obsvec - calcvec]
-    foreach vec {obsvec calcvec diffvec} {
+    #diffvec set [obsvec - calcvec]
+    foreach vec {obsvec calcvec} {
         # probably not needed with recent versions of BLT:
         global $vec
@@ -450 +456 @@
 }
 
+set ::topasfile ""
+proc get_topas_file {} {
+    set ::topasfile [tk_getOpenFile -title "Select Topas File" -parent . \
+                         -defaultextension .ascii \
+                         -filetypes {
+                             {"Topas ascii export" ".ascii"}
+                             {"all files" "*"}
+                         }]
+    if {$::topasfile == ""} return
+    if {[catch {set input [open $::topasfile r]} errmsg]} {
+        MyMessageBox -parent . -title "Open Error" \
+            -message "An error occured trying to open file $::topasfile: $errmsg" \
+            -icon error -type Ignore -default ignore
+        set ::topasfile ""
+        return
+    }
+    close $input
+    readdata .g
+}
+
+proc readdata_topas {box} {
+    global expgui expnam reflns graph
+    global lasthst
+    global hst peakinfo xunits weightlist
+    #set file "liveplot_output.ascii"
+    if {$::topasfile == ""} return
+    if {[catch {set input [open $::topasfile r]} errmsg]} {
+        MyMessageBox -parent . -title "Open Error" \
+            -message "An error occured trying to open file $::topasfile: $errmsg" \
+            -icon error -type Ignore -default ignore
+        return
+    }
+
+    $box config -title "(TOPAS import in progress)"
+    update
+    # parse the output of a file
+    set lasthst $hst
+    # initalize arrays
+    set num -1
+    set xlist {}
+    set obslist {}
+    set calclist {}
+    set bcklist {}
+    set xunits {}
+    set weightlist {}
+    global refhkllist refphaselist refpos
+    set refhkllist {}
+    set refphaselist {} 
+    set refpos {}
+    # define a list of reflection positions for each phase
+    for {set i 1} {$i < 10} {incr i} {
+        set reflns($i) {}
+    }
+    set i 0
+    while {[gets $input line] >= 0} {
+        incr i
+        if {[string first ":" $line] != -1} continue
+        # run update every 50th line
+        if {$i > 50} {set i 0; update}
+        if {[llength $line] == 5} {
+            scan $line %e%e%e%e%e X d Iobs Icalc Isig
+            if {$Isig > 0} {
+                if {$graph(xunits) == 0} {
+                    lappend xlist $X
+                } elseif {$graph(xunits) == 1} {
+                    lappend xlist $d
+                } else {
+                    lappend xlist [expr {6.283185307179586 / $d}]
+                }
+                lappend obslist $Iobs
+                lappend calclist $Icalc
+                #lappend bcklist 0
+                lappend weightlist [expr {1./($Isig * $Isig)}]
+            }
+        } elseif {[llength $line] == 7} {
+            scan $line %e%e%e%e%e%e%d h k l m d tt ph
+            if {$graph(xunits) == 0} {
+                set x $tt
+            } elseif {$graph(xunits) == 1} {
+                set x $d
+            } else {
+                set x [expr {6.283185307179586 / $d}]
+            }
+            set ph [expr {int($ph)}]
+            lappend reflns($ph) $x
+            lappend refhkllist "$h,$k,$l"
+            lappend refphaselist $ph 
+            lappend refpos $x
+        } elseif {[llength $line] == 3} {
+            scan $line %e%e%e x d b
+            lappend bcklist $b
+        } else {
+            puts "unexpected input: $line"
+        }
+    }
+    close $input
+
+    if {$graph(xunits) == 0} {
+        set xunits "2-Theta"
+    } elseif {$graph(xunits) == 1} {
+        set xunits "d"
+    } else {
+        set xunits "Q"
+    }
+    foreach elem [$box element names] {
+        eval $box element config $elem $graph(ElementShowOption)
+    }
+    xvec set $xlist
+    obsvec set $obslist
+    calcvec set $calclist
+    bckvec set $bcklist
+    #diffvec set [obsvec - calcvec]
+    refposvec set $refpos
+    set ::expmap(phaselist) [lsort -unique $refphaselist]
+    RegisterPhases $::expmap(phaselist)
+    if {$expgui(autotick)} {
+        foreach i $::expmap(phaselist) {
+            set peakinfo(flag$i) 1
+        }
+    }
+    #wifdvec length 0
+    # if {$graph(chi2)} {
+    #     wifdvec set $WGT
+    #     wifdvec set [wifdvec * diffvec]
+    #     wifdvec set [wifdvec * diffvec]
+    #     # now do a running sum
+    #     set sum 0
+    #     set sumlist {}
+    #     foreach n [wifdvec range 0 end] {
+    #         set sum [expr {$sum + $n}]
+    #         lappend sumlist $sum
+    #     }
+    #     wifdvec set $sumlist
+    #     wifdvec set [wifdvec / [wifdvec length]]
+    # } elseif {$graph(OmCoS)} {
+    #     wifdvec set $WGT
+    #     wifdvec expr sqrt(wifdvec)
+    #     wifdvec set [wifdvec * diffvec]
+    # }
+    if $graph(backsub) {
+        obsvec set [obsvec - bckvec]
+        calcvec set [calcvec - bckvec]
+    }
+    foreach vec {obsvec calcvec} {
+        # probably not needed with recent versions of BLT:
+        global $vec
+        # sometimes needed for latest version of BLT (2.4z)
+        catch {$vec variable $vec}
+    }
+    ApplyMag
+    plotdata
+}
+
 proc SetTitle {} {
     set bx .title
@@ -572 +731 @@
     global expnam hst peakinfo xunits yunits cycle reflns modtime
     global lasthst graph expgui box
-    global obsvec calcvec diffvec 
-
-    if {$graph(yunits) == 2} {
+    global obsvec calcvec diffvec bckvec
+
+    if {$graph(yunits) == 0} {
+        diffvec set [obsvec - calcvec]
+        $box element config 1 -label bckgr -line 1 -hide 0
+        $box element config 4 -label diff  -line 1 -hide 0
+    } elseif {$graph(yunits) == 1} {
+        diffvec set [obsvec - calcvec]
+        $box element config 1 -label bckgr -line 1 -hide 0
+        $box element config 4 -label diff  -line 1 -hide 0
+    } elseif {$graph(yunits) == 2} {
         set yunits {Intensity/sigma(I)}
         wifdvec set $::weightlist
@@ -584 +751 @@
         wifdvec set {}
         $box element config 1 -label {} -line 0 -hide 1
+        $box element config 4 -label diff  -line 1 -hide 0
+    } elseif {$graph(yunits) == 3} {
+        bckvec expr 0*bckvec
+        set msg {}
+        if {[set calcvec(min)] <= 0} {
+            if {$msg != ""} {append msg ", "}
+            append msg "calculated" 
+        }
+        if {[set obsvec(min)] <= 0} {
+            if {$msg != ""} {append msg " & "}
+            append msg "observed" 
+        }
+        if {$msg != ""} {
+            MyMessageBox -parent . -title "Invalid Range" \
+                -message "Log computation impossible due to zero or negative $msg intensity values" \
+                -icon warning -type Continue -default continue
+        } else {
+            set yunits {log(Intensity)}
+            obsvec expr log10(obsvec)
+            calcvec expr log10(calcvec)
+            if {[set bckvec(min)] <= 0} {
+                bckvec set {}
+                $box element config 1 -label {} -line 0 -hide 1
+            } else {
+                bckvec expr log10(bckvec)
+                $box element config 1 -label bckgr -line 1 -hide 0
+            }
+            diffvec set {}
+            $box element config 4 -label {} -line 0 -hide 1
+        }
     } else {
         $box element config 1 -label bckgr -line 1 -hide 0
+        $box element config 4 -label diff  -line 1 -hide 0
     }
 
@@ -691 +889 @@
         }
     }
-    # offset the difference pattern
-    set maxdiff  [set diffvec(max)]
-    if {$expgui(autotick)} {
-        diffvec set [diffvec + [expr {$cmin - $maxdiff}]]
-    } else {
-        diffvec set [diffvec + [expr {$cmin - 1.1*$maxdiff}]]
-    }
-    diffvec notify now
-
+    catch {
+        # offset the difference pattern
+        set maxdiff  [set diffvec(max)]
+        if {$expgui(autotick)} {
+            diffvec set [diffvec + [expr {$cmin - $maxdiff}]]
+        } else {
+            diffvec set [diffvec + [expr {$cmin - 1.1*$maxdiff}]]
+        }
+        diffvec notify now
+    }
     # force an update of the plot as BLT may not
     $box config -title [$box cget -title]
@@ -2156 +2355 @@
     .a.file.menu.export add command -label "to PDF" -command ExportPDF
 }
+
+.a.file.menu add command -label "Import from Topas" \
+    -command {get_topas_file}
 
 .a.file.menu add command -label Quit -command "destroy ."
@@ -2366 +2568 @@
     .g marker create line -coords "$xl -Inf $xl Inf" -name mag[incr i]
     .g marker create text -coords "$xl Inf" -name mag[incr i] -text "x$ym" -anchor w
-    foreach vec {obsvec calcvec bckvec diffvec} {
+    foreach vec {obsvec calcvec bckvec} {
         global $vec
         $vec expr {$vec * ymult}
@@ -2522 +2724 @@
     .a.options.menu.yunits add radiobutton -label "I/Sigma(I)" \
             -variable graph(yunits) -value 2 \
+            -command {set cycle [getcycle];readdata .g}
+    .a.options.menu.yunits add radiobutton -label "log(I)" \
+            -variable graph(yunits) -value 3 \
             -command {set cycle [getcycle];readdata .g}
     .a.options.menu add command -label "HKL labeling" -command setlblopts
@@ -2712 +2917 @@
 }
 
-expload $expnam.EXP
-mapexp
-if {$expgui(autotick)} {
-    foreach i $::expmap(phaselist) {
-        set peakinfo(flag$i) 1
-    }
-}
-        
+if {$expnam != ""} {
+    expload $expnam.EXP
+    mapexp
+    if {$expgui(autotick)} {
+        foreach i $::expmap(phaselist) {
+            set peakinfo(flag$i) 1
+        }
+    }
+} else {
+    mapexp
+}
+
 # fill the histogram menu
 if {[llength $expmap(powderlist)] > 15} {
@@ -2770 +2979 @@
 }
 
-foreach num $expmap(phaselist) {
-    .a.file.menu.tick add checkbutton -label "Phase $num" \
+proc RegisterPhases {phaselist } { 
+    foreach num $phaselist {
+        .a.file.menu.tick add checkbutton -label "Phase $num" \
             -variable  peakinfo(flag$num) \
             -command plotdata
-    if {$program != "bkgedit"}  {
-        bind . <Key-$num> ".a.file.menu.tick invoke [.a.file.menu.tick index end]"
-    }
-    .a.options.menu.tick add command -label "Phase $num opts" \
+        if {$::program != "bkgedit"}  {
+            bind . <Key-$num> ".a.file.menu.tick invoke [.a.file.menu.tick index end]"
+        }
+        .a.options.menu.tick add command -label "Phase $num opts" \
             -command "minioptionsbox $num"
-}
+    }
+}
+RegisterPhases $expmap(phaselist)
 
 # N = load next histogram