Demeter/Athena/Artemis To Do List

• [ ] Dispersive algorithm, include in Athena
• [X] S02 display issue
• [ ] clone data sets and path lists in Artemis
• [X] Artemis history improvments
• [X] xkcd style plots, see http://tex.stackexchange.com/questions/74878/create-xkcd-style-diagram-in-tex and http://rfonseca.github.io/xkcd-gnuplot/ and http://antiyawn.com/uploads/humorsans.html
• [ ] plot key for neg part of envelope is incorrect

• [ ] From Joel Ullom: In our data, the error bar in each energy bin of the EXAFS spectrum is known from Poisson statistics since the photons are (laboriously) counted one by one. This creates the opportunity to propagate these errors through the Artemis fitting process. Potentially, the resulting error bars on the fit parameters are more meaningful. This software capability would be interesting to explore. This is a Larch chore
• [X] From Joel Ullom: In the rebinning functionality of Athena, all rebinnings reduced the amplitude of the white line feature in our ferrioxalate data. You explained well why rebinning is seldom useful when using a conventional EXAFS energy grid. However, we only reproduce the conventional energy grid through rebinning so I think rebinning is still relevant for us. It would be nice to be able to rebin without reducing spectral detail in the XANES region. – What is the width of the box?
• [X] 5 and 6 legged paths
• [ ] PCA improvements
• [ ] feff8.5L
• [X] persistance of analysis methods in Athena This can be implemented in the same way I implemented XDI persistance – for each group, serialize a blessed scalar and write that to the record

• Xray/Absorption/CL.pm – this needs to be refactored
• t/ tests need to be tested with Larch
• in particular, need a t/001_larch.t test (with an appropriate SKIP in case of no server)
• “nergy”: XDAC vs. Ifeffit. Larch will see “energy”.
  • Perhaps a larch or ifeffit configuration attribute

  • ack-ing for ’\bnergy\b’ yields:

    examples/recipes/MultiChannel/mc2prj
    54:  #my @energy    = $mc->get_array('nergy');
    
    lib/Demeter/Plugins/10BMMultiChannel.pm
    53:    my @energy = $mc->get_array('nergy');
    
    lib/Demeter/Plugins/X23A2MED.pm
    324:becomes "nergy".  Go figure.
    
    lib/Demeter/Plugins/x23a2med.demeter_conf
    10:default=nergy
    

• Need to add Larch copyright statement throughout

  ##             Larch is copyright (c) 2013 Matt Newville, Tom Trainer
  ##                                 http://xraypy.github.io/xraylarch/
  

• [X] why does Wx::FileDialog with wxFD_OVERWRITE_PROMPT style not work correctly? see https://bugzilla.gnome.org/show_bug.cgi?id=631908 and https://bugs.launchpad.net/ubuntu/+source/gtk+2.0/+bug/558674 for more info Turns out this is a gtk problem – I can make the same thing happen with Firefox! This is now deprecated.

• [X] Relocation needs testing on Windows, need to make sure that the executables can all be found,
• [X] also need to be able to find all of Ifeffit CL and CAPS files.

• [ ] in Demeter::Data::IO::save_many, why doesn’t updating in n specifying “background” not work to bring data up to date? (fft, i.e. doing autobk, does work)
• [ ] tie multiple groups together (e.g. MED data with reference)
• [ ] config param updated AND that param is currently showing in the Prefs tool – need to update display in Prefs tool
• [ ] add a record to an existing Athena project file
• [ ] clnorm + Julia and Jingen’s MBACK replacement
• [ ] Data object should note that datatype is xanes and not compute fbkg since the bkg array does not exist
• [ ] cannot specify title for stddev and variance plots
• [ ] Demeter command backend needs lots of polishing
• [ ] 3rd derivative
• [ ] SDK: better documentation for freeze/thaw//serialize/deserialize
• [ ] error check deserialization for all objects, verify that it is a yaml or whatnot, return 0 if not
• [ ] OpenBabel interface, tied into Feff
• [ ] MRU lists and unicode, unicode-y file paths fail the -e test at Demeter::MRU line 77
• [ ] Feff8 integration
• [ ] Use PDL in pathfinder
• [ ] background groups for AXAFS
• [X] Add tests to Path ranking framework (Karine Provost’s idea, implemented in Demeter)
• [X] serialize VPath, put VPath into dpj and fpj files
• [X] set E0 to peak of white line
• [X] need to disable indicators during the Rk plot. Indicators (as implemented) are not consistent with multiplot
• [X] Plucking from gnuplot really sucks

• Need to expand the filetype system by examining data from all the XAS beamlines in the world. Yes … all of them.
• solicit help from the facility representatives

• [X] parameter group context menus don’t get posted (see http://www.nntp.perl.org/group/perl.wxperl.users/2011/03/msg7929.html)
• [ ] the frickin’ Gnuplot error logs seem to remain open and locked on Windows when a crash happens
• [ ] status bar does not get color for wait or error messages this may be unfixable, see http://www.nntp.perl.org/group/perl.wxperl.users/2011/04/msg7943.html
• [ ] The atoms panel background color is too light. Which window needs its BackgroundColour set to wxNullColour?
• [ ] clampbox does not get enabled/disabled explicitly, is this another aspect of StaticBox that is different on Windows? (see link above)
• [ ] Need to test that paths with (parens|commas|quotes) get followed correctly in all situations
• [X] Initial initialization of gnuplot and feff executable locations in the situation where the package has been moved or reinstalled such that and old demeter.ini still exists
• [X] relocation of Strawberry leaves Ifeffit unable to find phase shift and CL tables (use an ENV variable?)
• [X] The Strawberry+Demeter package does not coexist at all with ActivePerl. Best solution is to generate ppd for Demeter armed with all dependencies. Would need to compile wrapper and somehow get gnuplot on the machine. Solved by explicitly calling Strawberry in the .bat files

More standards!!

• [ ] Structural Units
  • Extension of VPath
  • Store GDS, feff, and path objects in a zip file.
  • On import, mark GDS parameters as merge if in conflict
• [ ] MSPaths
  • Much like SSPath, make an arbitrary n-legged path
• [ ] Nearly collinear paths, ThreeBody
  • Extension of VPath
  • need to worry about load order in Demeter.pm
  • Define a three body configuration, generate its 4-legged path and a sequence of three-legged paths along with a mixing parameter.
  • It will take a single set of path parameters that are pushed onto the generated Path objects, except for the amplitude, which will be computed from the mixing parameter.
  • This is a single object for the user to interact with which expands into 2 or 3 3-legged paths and a single 4-legged path

• [ ] CIF issue: CIF file with “_eof” token at end of file, as in this cif file
• [ ] Handle CIF import problems more gracefully (See Shelly’s other email from 17 June 2011)
• [ ] CIF errors are not handled gracefully (e.g. multiple occupancy)

• [ ] Parsing an atoms.inp file for the space group is fragile. It currently grabs the 13 characters following the equals sign and white space. 13 is the longest standard HM symbol with a modifier – an example is ’I 41/a m d :1’ (see http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif as an example). However, if additional spaces are present or if another keyword follows in fewer than 13 characters, the parser will do the wrong thing.
• [X] Setting of Ba2Co9O14 (Chanapa Kongmark), also some problem with ZnFe2O4
• [X] should be a way to insert tabulated shift vector, if it exists
• [X] handle “: setting” notation: :R, :H, :1, :2 (for example)
  • :1 and :2 seem to have to do with whether the shift vector should be used, see ZnFe2O4.cif and use the shift vector
  • :R, :H specify rhombohedral or tri/hexagonal setting
• [X] Lepidocrocite issue (amam gets changed to cmcm)
• [ ] 2 sites at the same position with occupancies <1. see file above for an example
• [ ] George Sterbinsky’s mailing list post that turned out to be about atoms’ sphere and rhomboid in a non-orthogonal group
• [ ] very confusing error message when core is not a tag
• [X] Shell tags in the feff.inp ATOMS list
• [X]

  Rhombic groups seem not be handled properly. This example fails to generate a subshell of 3 atoms at ~1.9A

  title name:     Fe2O3  hematite
  space  R -3 c
  a    = 5.0380   b    = 5.0380   c    = 13.7720
  rmax = 6.00     core = Fe1
  atom
    Fe     0.00000   0.00000   0.35530  Fe1
    O      0.30590   0.00000   0.25000  O1
  

• [X]

  This input data fails

  title formula:  LaCoO3
  title refer1:  PRB V. 66 P. 094408 (2002)
  title notes:   T = 300 K
  space  r -3 c
  a = 5.44864       c = 13.1035
  rmax = 6.00       core = Co1
  atom
    Co     0.00000   0.00000   0.00000  Co1
    La     0.00000   0.00000   0.25000  La1
    O      0.55032   0.00000   0.25000  O1