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Bugs and limitations in Xray::BLA and Metis

Top of the TODO list [1/10]

  1. [X] Capture BLA and Pilatus metadata, display on XDI page capture BLA.xesimage
  2. [ ] Take a project to a fresh location which lacks the image files, verify that it works
  3. [ ] Flag images for not including in an XES merge or for excluding from a HERFD (i.e. deglitching)
  4. [ ] Reuse masks button for RXES Data page
  5. [ ] Reuse masks buttons and better checks for up-to-date-ness. Better back calculating of needed masks
  6. [ ] weak mask can lead to 0 illuminated pixels. Need a good check for this. See NbN
  7. [ ] Don’t save shield to HDF5 file if not using shield in recipe
  8. [ ] gzip the project file, it’s a factor of 10 to 20
  9. [ ] Change mode, for example start in HERFD mode, import an XES project file
  10. [ ] In Config, “apply” and “apply+save” do the same thing

From Feb 2016 experiment

  • [X] Need to generalize how XES spectrum is made in terms of how the XES measurement image is selected. This experiment has a couple different examples of needing to specify a measurement image with having a scan file. See –xesimage in bla.
  • [X] Jeremy’s Lv thing, like the _v Bi measurements. make the shield start, say, 3 back. Do it in regions, changing parameters as needed. See Lv.ini.
  • [X] Capture exposure time from pilatus metadata
  • [X] Track metadata about sample through bla ini file (with TextCtrl in metis)
  • [X] Need to integrate shield into workflow much more tightly, switch in GUI to turn it on. The under-the-hood workflow will necessarily be the same:
    1. Run through mask creation
    2. Run through shield creation
    3. Re-run mask creation with shields
    4. Make XES with shielded masks

Issues with Xray::BLA [10/18]

  • [ ] More robust error handling.
  • [ ] energy in mask file name is awkwardly handled at Xray::BLA::IO lines 45-46
  • [X] When a mask processing step results in 0 illuminated pixels, Metis crashes. Should reset working_image to prior state if 0 pixels illuminated.
  • [ ] More testing.
  • [ ] Use the energy map to create a mask with a specified energy width.
  • [X] In the future, will need a more sophisticated mechanism for relating C<stub> to scan file and to image files – some kind of templating scheme, I suspect
  • [ ] Parse columns of scan file and patern match to find the useful columns. Too much assumption goes into the scan method. Also will need a flag to say whether conventional data was gathered from the scan file. Also need a way to choose between transmission and conventional fluorescence, which may be done with an SDD.
  • [X] Drop current crop of gnuplot+Text::Template methods in favor of PDL::Graphics::Gnuplot. or not -- it's handy to write out the .gp file.
  • [X] gnuplot file for rixs map – how is this done in PDL? PDL has linear axis transforms, but can it do non-linear transforms specified point-by-point?
  • [X] Other energy map output formats. A gif would be useful. (Much easier using PDL)
  • [ ] consider using MooseX::GetSet
  • [ ] It should not be necessary to specify the list of elastic energies in the config file. They could be culled from the file names or from a file of metadata. (As in Metis)
  • [X] Figure out element and emission line by comparing the midpoint of the range of elastic energies to a table of line energies.
  • [X] Use of XDI is undocumented. And incomplete. And, frankly, Xray::XDI needs attention.
  • [X] Think about how to use HDF5 to store images, scans, scan metadata, and Xray::BLA metadata.
  • [ ] Configurable data columns – need to be more flexible about content of scan file. Also need to be able to configure column with conventional XAFS for mu(E) plot. See Xray/BLA.pm line 568, loop over energy points in scan method.
  • [X] Maybe use object oriented plotting interface ....
  • [X] Athena project output from rixs task

Issues with Metis [11/17]

  • [X] Version 2 will have Xray::BLA objects for each emission energy and one for the aggregate object. That will make XES and RIXS much simpler to implement sensibly. Will also allow me to dump the working_image concept.
  • [X] implement XES and RIXS
  • [X] replot RIXS & export Athena project file from RIXS
  • [X] flag whether steps have changed, don’t recompute masks for XES at a different incident energy
  • [X] Resetting a mask leads to crashy trouble – need to investigate
  • [ ] implement map and mapmask
  • [X] implement aggregate mask from set of elastic images
  • [ ] separate stubs for elastic and data images (partially addressed by file name templates)
  • [X] widgets for selecting folders. Wx::FileDialog was causing crashes on my home computer.
  • [X] More error checking, edge cases. For example, what happens when a stub + folders does not return a sensible pile of stuff?
  • [ ] mask development animations. according to the PERLDL mailing list, giving file.gif to wmpeg will cause it to write an animated gif, assuming ffmpeg is installed on the computer. this needs testing outside of metis.
  • [ ] animation of mask vs. elastic energy
  • [X] some kind of system for specifying file naming patterns – this is somewhat less important now that the contents of the elastic and image lists on the Files tool are used explicitly. if this is still ambiguous, a file selection dialog can be used to select content for the lists.
  • [X] Persistance. Need to save group of masks. Need to save aggregate mask. Need to reimport them.
  • [ ] how are element and line used? (answer: they are used to set the white color band in a map)
  • [ ] Click on image list, show incident energy of that image in the status bar
  • [X] Save metadata from .ini file to RIXS prj file

Mask algorithm possibilities

  • proper edge detection
  • Fourier filtering