Changeset 1115

Timestamp:

Feb 26, 2011 9:47:37 PM (13 years ago)

Author:

toby

Message:

scan .EXP files for GENLES blowups; update web pages

Location:

branches/sandbox

Files:

• doc/expgui.html (modified) (13 diffs)
• doc/expgui_intro.html (modified) (4 diffs)
• expgui (modified) (5 diffs)
• gsascmds.tcl (modified) (6 diffs)
• readexp.tcl (modified) (4 diffs)

branches/sandbox/doc/expgui.html

@@ -16 +16 @@
 EXPGUI<BR>
 A Graphical User Interface for 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 <HR noshade width="75%" size="2" align="center">
@@ -34 +34 @@
 <P><P>
 EXPGUI is a graphical interface for the 
-Los Alamos
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
-GSAS</A> package. 
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">GSAS</A>
+package, developed at Los Alamos and maintained now at Argonne. 
 EXPGUI does two things: 
 it can be used to directly modify the GSAS 
@@ -117 +116 @@
 A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", 
 Los Alamos National Laboratory Report LAUR 86-748 (2000).
-<A HREF="http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/gsas/public/gsas/manual/GSASManual.pdf">
+<A
+  HREF="https://subversion.xor.aps.anl.gov/EXPGUI/gsas/all/GSAS%20Manual.pdf">
 [link to PDF copy of manual]
 </A>
@@ -154 +154 @@
 are used. The File/Save operation is done automatically before any GSAS
 programs, such as GENLES or EXPEDT, are run.
+<P>
+<A name="badexp">
+The GSAS refinement program, GENLES, will sometimes "blow up", where the
+  program changes varied parameters to values very far from their
+  correct values. This occurs when parameters are highly correlated,
+  are refining to values that are not allowed, or some of the refined parameters have
+  very little impact on the quality of the fit. When this happens,
+  invalid values are written to the GSAS experiment file that contain
+  either asterisks (****) or the string "NAN" (not a number). Such
+  files cannot be used for additional GENLES runs.
+  <P>
+  When EXPGUI reads a .EXP file it scans it for evidence of a previous
+  failure of a GENLES refinement and warns if a problem is
+  noted. Please note that this scan is not perfect and occasionally
+  you may be warned in cases where the file is fine (if possible,
+  please send such .EXP file to Brian Toby so this scan can be improved.)
+  When such a "bad" .EXP file is located, one can "revert" to an
+  archived copy of a previous experiment file (with suffix .Oxx). This
+  can be done with the Revert menu item in the File menu. Note that
+clicking on a file in the file selection window causes it to be
+scanned and shows the status of that refinement. Also note that
+usually the last good archived file has settings that will produce the same bad
+refinement, so it is necessary to either revert further back, or to
+change the refinement options before running GENLES. 
 <P>
 
@@ -681 +705 @@
 <A name=tcltk>
 <H2>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk</A></H2>
 The 
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
+<A Href="http://www.tcl.tk">
 Tcl/Tk program</A> is a platform-independent scripting language that is
 used to implement most of EXPGUI. This software is available for free
-and must be loaded in order to use EXPGUI. See the 
-installation notes for 
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for information on how to do this.
+and must be loaded in order to use EXPGUI. A somewhat out of date
+version of Tcl/Tk (8.4) is distributed with EXPGUI (ncnrpack.exe, etc.) but
+more recent versions can be used, but note that the BLT package (see
+below) is needed for all features of EXPGUI.
 While learning Tcl/Tk is a great thing to do, it is not a requirement
 for using or installing EXPGUI.
-
-<A name=winexec>
-<H3>
-WINEXEC</H3>
-<UL>
-The WINEXEC package is needed under Windows-95 and its offspring 
-(-98 and -ME). See the <A HREF="expgui_Win_readme.html">Windows installation 
-notes</A> for more details.
-</UL>
 
 <A name=blt>
@@ -715 +729 @@
 If this is the case, a message, 
 "BLT Setup Error: could not access a Blt_ routine...", will be displayed.
-This is most common in UNIX and is discussed further in the 
-<A HREF="expgui_Unix_readme.html">UNIX installation notes</A>. Also see 
-<A HREF="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">
-http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html
-</A> for more information on installation of BLT.
+Use of the ncnrpack file distributed with EXPGUI usually avoids this problem.
 </UL>
 
@@ -727 +737 @@
 <UL>
 The
-<A HREF="www.hume.com">Hume 
+<A HREF="http://www.hume.com">Hume 
 </A>
 Linear Algebra Tcl Package, 
-<A HREF="www.hume.com">
+<A HREF="http://www.hume.com/la/la.html">
 La</A>, 
 is used by the BKGEDIT
@@ -739 +749 @@
 should not happen, since the package is included with the EXPGUI files.
 So if get this error you probably have an incomplete installation.
-Note that the La package requires Tcl/Tk version 8.1 or higher, so that if 
-you are using an older version of Tcl/Tk, you will need to upgrade.
-See the installation instructions for
-<A HREF="expgui_Win_readme.html">Windows</A>,
-and for
-<A HREF="expgui_Unix_readme.html">UNIX</A> for more information on Tcl/Tk.
+</UL>
+
+<A name=winexec>
+<H3>
+WINEXEC</H3>
+<UL>
+The WINEXEC package was needed under Windows-95 and its offspring 
+(-98 and -ME). It was found in older versions of EXPGUI, but is no
+  longer included.
 </UL>
 
@@ -750 +763 @@
 Acknowledgments</H2>
 Praise to Larson and 
-Von Dreele for GSAS, <A HREF="http://www.scriptics.com/">Ousterhout</A>
+Von Dreele for GSAS, <A HREF="http://home.pacbell.net/ouster/">John Ousterhout</A>
 for Tcl/Tk, 
-Przemek Klosowski</A>
+Przemek Klosowski
 for convincing me to learn Tcl/Tk 
-and Jonathan Wasserman for helping get this project started.
-Thanks also to 
+and Jonathan Wasserman for helping me get this project started.
+Thanks also to
+Charles Lake of Indiana University of PA for working on many recent additions to EXPGUI, including the
+bond-distance restraints module and the (soon to come) rigid body editor;
 Pamela Whitfield of the NRC (Canada) for writing large 
 sections of the 
@@ -763 +778 @@
 code and to John Cowgill for the "Export to GRACE" code.
 <P>
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/gsas.html">
+<A Href="https://subversion.xor.aps.anl.gov/trac/EXPGUI/wiki/GSASIntro">
 GSAS</A>
 is written by Allen C. Larson and Robert B. Von Dreele while at 
@@ -770 +785 @@
 <A HREF="MAILTO:vondreele@anl.gov">vondreele@anl.gov</A>
 EXPGUI was written by Brian H. Toby while at the NIST Center for Neutron Research,
-<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A> 
-with help from Jonathan Wasserman.
+<A HREF="MAILTO:Brian.Toby@ANL.GOV">Brian.Toby@ANL.GOV</A>.
 
 <P><hr><blockquote>
@@ -786 +800 @@
 software.
 
-<P>The author of EXPGUI is a U.S. Government employee which means that
+<P>EXPGUI was written by a U.S. Government employee, which means that
 EXPGUI is not subject to copyright. Have fun with it. Modify it. Please write 
 new sections and make them available to the rest of the world. 
@@ -793 +807 @@
 expressed or implied, or assumes any liability or responsibility 
 for the use of this information or the software described
-here. Brand names cited herein are used for
-identification purposes and do not constitute an endorsement by NIST.
+here.
 </blockquote>
 

branches/sandbox/doc/expgui_intro.html

@@ -70 +70 @@
 Customization notes</A>
 <LI>
-<A HREF="tutorial3/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial3/index.html">
 A well-annotated CW neutron tutorial (Alumina).</A>
 <B><I>A very good place to start!</I></B>
 <LI>
-<A HREF="tutorial1/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial1/index.html">
 A TOF Tutorial Example (Nickel)</A>
 <LI>
-<A HREF="tutorial2/index.html">
+<A HREF="https://subversion.xor.aps.anl.gov/EXPGUI/tutorials/tutorial2/index.html">
 A CW Neutron Tutorial Example (Garnet)</A>
 </UL>
@@ -164 +164 @@
 <p><br><B>Who is to blame for EXPGUI?</B>
 <blockquote>The initial version of the GUI part of EXPGUI was created by
-Jonathan Wasserman (thanks Jon!) <a href="http://www.ncnr.nist.gov/staff/toby/">Brian
+Jonathan Wasserman (thanks Jon!) Brian
 Toby</a> is irresponsible for the rest.</blockquote>
 
@@ -170 +170 @@
 <blockquote>Gee, you want to add some features... Great! You have all the
 EXPGUI sources and
-<A Href="http://www.ncnr.nist.gov/programs/crystallography/software/tclpkgs.html">Tcl/Tk</A>
-is free. Oh, you want me to do it. Well, please 
+Tcl/Tk is free. Oh, you want me to do it. Well, please 
 ask and I will try. In particular, I am looking for good ideas on 
 how to design GUI's for different aspects of experiment editing, 
@@ -177 +176 @@
 
 <p><br><B>Mailing List</B>
-<blockquote>If you would like to get news about EXPGUI, please send 
-<a href="mailto:brian.toby@anl.gov?subject=EXPGUI Mailing List">Brian.Toby@ANL.GOV</a> e-mail. The mailing list is not active at present, but 
-I hope to use it again to provide 
+<blockquote>If you would like to get news about EXPGUI, please 
+<a href="http://www.aps.anl.gov/mailman/listinfo/expgui">see this
+link</a>.
+The mailing list is used only to provide 
 information about updates and bug fixes. 
 </blockquote>

branches/sandbox/expgui

@@ -1 @@
-#!/bin/sh
+#!/bin/sh 
 # the next line restarts this script using wish found in the path\
 exec wish "$0" "$@"
@@ -157 +157 @@
 # setup DISAGL viewer & editor
 source [file join $expgui(scriptdir) disagledit.tcl]
-source [file join $expgui(scriptdir) geo_viewer.tcl]
+source [file join $expgui(scriptdir) Geo_Viewer.tcl]
 #---------------------------------------------------------------------------
 # override options with locally defined values
@@ -406 +406 @@
     # start checking for external changes
     afterawhile
+    # check if the file seems corrupt
+    set warnings [ScanEXPforError]
+    if {$warnings != ""} {
+        ExplainEXPerror . $warnings $expfile
+    }
 }
 
@@ -548 +553 @@
         set expgui(curhist) {}
     }
-    if {[CountHistory] > 100} {
-        DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
-    }
+#    if {[CountHistory] > 100} {
+#       DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
+#    }
 }
 
@@ -4519 +4524 @@
 update
 SetStartPanel
-if {[CountHistory] > 200} {
-    DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
-}
+#if {[CountHistory] > 200} {
+#    DeleteHistoryRecords "This .EXP file has [CountHistory] history records\nErasing most will speed EXPGUI"
+#}

branches/sandbox/gsascmds.tcl

@@ -1026 +1026 @@
             }
         }
-        # so sorry, have to use Internet Explorer
+        # so sorry, have to use Safari, even if not default
         set url [file nativename $url]; # replace ~/ if present
         if {[file pathtype $url] == "relative"} {
             set url [file join [pwd] $url]
         }
-        exec osascript -e "tell application \"Internet Explorer\"\rGetURL \"file://$url\"\rend tell"
+        exec osascript -e "tell application \"Safari\" to open location \"file://$url\""
     } elseif {$tcl_platform(platform) == "unix"} {
         set browserlist {}
@@ -2696 +2696 @@
     return
 }
+
+proc ScanEXPforError {"ns {}"} {
+    # record types to ignore
+    set ignorelist {DESCR HSTRY PNAM HNAM "REFN STATS"}
+    set warn {}
+    set badkeylist {}
+    # scan file for warnings
+    foreach key [array names ${ns}::exparray] {
+        if {[string first "***" [set ${ns}::exparray($key)]] != -1 || 
+            [string first "nan" [set ${ns}::exparray($key)]] != -1 ||
+            [string first "NAN" [set ${ns}::exparray($key)]] != -1 
+        } {
+            #puts [set ${ns}::exparray($key)]
+            set OK 0
+            foreach i $ignorelist {
+                if {[string first $i $key] != -1} {
+                    set OK 1
+                    break
+                }
+            }
+            # ignore atom name section of Atom records
+            if {(! $OK) && [string match  "CRS*AT*A" $key]} {
+                foreach str [list [string range [set ${ns}::exparray($key)] 0 49] 
+                             [string range [set ${ns}::exparray($key)] 58 end]] {
+                    if {[string first "***" $str] || [string first "nan" $str] || [string first "NAN" $str]} {
+                        append warn "  Record \"$key\": [set ${ns}::exparray($key)]\n"
+                        lappend badkeylist $key
+                        break
+                    }
+                }
+                continue
+            }
+            if {! $OK} {
+                append warn "  Record \"$key\": [set ${ns}::exparray($key)]\n"
+                lappend badkeylist $key
+            }
+        }
+    }
+    if {$warn == ""} return
+    set hint ""
+    set unknown ""
+    foreach key $badkeylist {
+        if {[string match  "CRS*AT*" $key]} {
+            if {[string first "atomic parameter" $hint] == -1} {
+                append hint "\t* An atomic parameter (coordinate, occupancy or U) appears out of range\n"
+            }
+        } elseif {[string match  "CRS*ABC*" $key] || 
+                  [string match  "CRS*ANGLES*" $key] || 
+                  [string match  "CRS*CELVOL*" $key]} {
+            if {[string first "cell parameter" $hint] == -1} {
+                append hint "\t* A unit cell parameter appears out of range\n"
+            }
+        } elseif {[string match  "CRS*ODF*" $key]} {
+            if {[string first "spherical harmonic" $hint] == -1} {
+                append hint "\t* A spherical harmonic (ODF) parameter appears out of range\n"
+            }
+        } elseif {[string match  "HST*ICONS" $key]} {
+            if {[string first "diffractometer constant" $hint] == -1} {
+                append hint "\t* A diffractometer constant (wave, DIFC,...) appears out of range\n"
+            }
+        } elseif {[string match  "HST*TRNGE" $key]} {
+            if {[string first "histogram data range" $hint] == -1} {
+                append hint "\t* A histogram data range value appears out of range\n"
+            }
+        } elseif {[string match "*GNLS  RUN*" $key] || 
+                  [string match "*GNLS SHFTS" $key] ||
+                  [string match "HST*RPOWD" $key] ||
+                  [string match " REFN RPOWD " $key] ||
+                  [string match " REFN GDNFT " $key]
+              } {
+            if {[string first "refinement statistics" $hint] == -1} {
+                append hint "\t* The refinement statistics imply the last refinement diverged\n"
+            }
+        } else {
+            lappend unknown $key
+        }
+    }
+    if {$unknown != ""} {
+        append hint "\t* The following less common problem record(s) appear out of range:\n\t\t"
+        foreach key $unknown {
+            append hint "\"" [string trim $key] "\" "
+        }
+    }
+    return "Likely error(s) noted:\n$hint\nDetails of problem(s):\n$warn"
+}
+
+proc ExplainEXPerror {parent message file} {
+    if {$parent == "."} {
+        set w .experr
+    } else {
+        set w $parent.experr
+    }
+    catch {destroy $w}
+    toplevel $w -class Dialog
+    wm title $w "Corrupt .EXP file"
+    wm iconname $w Dialog
+    wm protocol $w WM_DELETE_WINDOW { }
+    # Make the message box transient if the parent is viewable.
+    if {[winfo viewable [winfo toplevel $parent]] } {
+        wm transient $w $parent
+    } 
+    frame $w.bot
+    pack $w.bot -side bottom -fill both
+    frame $w.top
+    pack $w.top -side top -fill both -expand 1
+    frame $w.msg
+    pack $w.msg -in $w.top -side right -expand 1 -fill both -padx 3m -pady 3m
+    set txt {Likely errors were noted when reading this file}
+    append txt " ([file tail $file]). "
+    append txt "These problems probably\narose from the last refinement, "
+    append txt "based on settings applied in the previous saved file.\n"
+    append txt "It is probably not possible to continue with this file.\n"
+    append txt "You likely need to revert at least two archived versions back."
+    grid [label $w.msg.s -text $txt -justify left] -row 0 -column 0 -sticky nws
+    grid [button $w.msg.1 -text Help -bg yellow \
+              -command "MakeWWWHelp expgui.html badexp"] -row 0 -column 1 -columnspan 2 -sticky ne
+    bind $w <Key-F1> "MakeWWWHelp expgui.html badexp"
+    set filelist [lsort -dictionary -decreasing \
+                      [glob -nocomplain \
+                           [file root $file.O* ]]]
+    grid [text  $w.msg.t -font {Times 12} \
+              -height 10 -width 90 -relief flat -wrap word \
+              -yscrollcommand "$w.msg.rscr set" \
+             ] -row 1 -column 0  -columnspan 2 -sticky news
+    grid [scrollbar $w.msg.rscr  -command "$w.msg.t yview" \
+             ] -row 1 -column 2 -sticky ns
+    # give extra space to the text box
+    grid columnconfigure $w.msg 0 -weight 1
+    grid rowconfigure $w.msg 1 -weight 1
+    $w.msg.t insert end $message
+    button $w.ok -command [list destroy $w] -text OK -default active
+    pack $w.ok -in $w.bot -side left -expand 1 -padx 3m -pady 2m
+    putontop $w
+    tkwait window $w
+    afterputontop
+}
+
 proc UpdateInfoBox {} {
     global expgui
@@ -2702 +2839 @@
     set file [file join [set expgui(FileMenuDir)] $expgui(FileMenuEXPNAM)]
     if [file isdirectory $file] return
-    if [file exists $file] {
+    if [file exists $file] {    
         pack [label $expgui(FileInfoBox).1 -text $expgui(FileMenuEXPNAM)] \
                 -side top
         catch {
+            # load the EXP file into a namespace & scan for errors
+            expload $file scan
+            set warnings [ScanEXPforError scan]
+            if {$warnings != ""} {
+                pack [frame $expgui(FileInfoBox).1a -bg yellow -padx 4 -pady 4] -side top
+                pack [label $expgui(FileInfoBox).1a.err -justify left \
+                          -text "WARNING: Likely corrupt" -bg yellow] \
+                    -side left -anchor w -fill both
+                pack [button $expgui(FileInfoBox).1a.show \
+                          -text "More..." -padx 0 \
+                          -command "ExplainEXPerror $expgui(FileInfoBox) [list $warnings] $file"\
+                         ] -side right -anchor w
+            }
             set fp [open $file r]
             global testline
@@ -2716 +2866 @@
                     -text "last GENLES run:\n  $last\n  total cycles: $cycles"] \
                 -side top -anchor w
+            set chi2 ?
+            set vars ?
             regexp {REFN GDNFT.*= *([0-9]*\.[0-9]*) +for *([0-9]+) variables} \
                     $testline a chi2 vars
@@ -2754 +2906 @@
                     -text $lbl] \
                     -side top -anchor w     
-        }
+        } err
     }
 }
@@ -2864 +3016 @@
         if {$expgui(expfile) == [file join $expgui(FileMenuDir) $file]} {
             $files selection set $i
+            set expgui(FileMenuEXPNAM) $file
+            UpdateInfoBox
         }
     }

branches/sandbox/readexp.tcl

@@ -9 +9 @@
 # returns 1 if the file is 80 char/line + cr/lf
 # returns 2 if the file is sequential but not fixed-record length
-proc expload {expfile} {
-    global exparray tcl_platform
-    # $expfile is the path to the data file. 
-
+proc expload {expfile "ns {}"} {
+    # expfile is the path to the data file. 
+    # ns is the namespace to place the output array (default is global)
+    if {$ns != ""} {
+        namespace eval $ns {}
+    }
     if [catch {set fil [open "$expfile" r]}] {
         tk_dialog .expFileErrorMsg "File Open Error" \
@@ -27 +29 @@
     }
     catch {
-        unset exparray
+        unset ${ns}::exparray
     }
     if {$len > 160} {
@@ -39 +41 @@
             incr i2 80
             set key [string range $nline 0 11]
-            set exparray($key) [string range $nline 12 end]
+            set ${ns}::exparray($key) [string range $nline 12 end]
         }
     } else {
@@ -45 +47 @@
         while {$len > 0} {
             set key [string range $line 0 11]
-            set exparray($key) [string range $line 12 79]
+            set ${ns}::exparray($key) [string range $line 12 79]
             if {$len != 81 || [string range $line end end] != "\r"} {set fmt 2}
             set len [gets $fil line]