Priority To Do Items

• Image / ctr processing..
  • saving/restoring data - single hdf file for ctr object. (see notes below)
  • Make fcns for correcting 'bad pixels'. Add option on file reading to correct based on bad pixel map.
  • Speed up backgrounds
  • Add image hkl indexing
  • Add tracking for miscuts and auto rotate images
  • Polygon image rois?
  • Two image rois - one for bgr, 2nd for integration?
  • Add ave funcs (plane groups) to CTR data
  • Attenuation factors
  • Rocking scan integrations (peak module)

Detailed To Do List for tdl/modules

modules/fmtfiles

• work on simple file IO (column, xcel, etc.).
• generic interface for reading files from zip archive

modules/mpcutil

• more options for minimize function

modules/xray/ana

general

• specfile: function to list spec scans to screen (ie actual scans)
• Someplace we need methods for attenuator calcs ~ similar to deadtime...
• background: Add smoothing / rebin option for backgrounds and rewrite the slow part of in c to speed up
• create a peak module/class (move from mpcutils):
  • add fit method in python, make very similar to xrf.
  • then connect to c-library version, ie speed up fitting. would be great if c-code was generic enough so we could use it in peak module and swap out code in xrf modules to speed up fits there too!
  • numerical peak integrations
  • use background.background

scan_data

• work on append - especially sorting and combining data that is not of len = npts
• work on merge/average

• work on __set_item__

   note make some rules:
     - add_scans / subtract_scans:  
        * scalers, images, meds etc are added and subtracted (all must be same len)
        * might want to set rule so only unprocessed images/xrfs can be added and subtracted... 
        * positioners are stored as list scan_data.x = [x1,x2]
     - concat_scans
        * sort by scan axis

image_data

• read in bad pixel map file to apply to images (apply in reader)
• make roi box from arbitrary points (not just rectangle)
• convert images to recip space coordinates
  • therefore can calc rot angle to keep L projection along horizontal and model peak widths in order to improve automation of integration.
  • To do correctly need detector distance, pixel spacing, pitch, yaw and roll.
• Generate an algo for solving detector parameters:
  • Define pixel center at 0del and 0nu. then give direct beam pixel position at 4 different del and nu settings. From these refine distance and 3 angles. (note if do with diffraction peaks from known sample can also refine lambda and axis offsets...)

ctr_data

• incorporate ave functionality
• integrate / correct rocking scan data

save_data

• Save / restore methods for specific classes. (using pytables)

  • scandata or list of scandata objs -> saves scandata (and images etc) to a single hdf

  • ctr data -> incl scandata objects all in single file

  • xrf
  • gimodel
  • etc...
• note with scandata or ctr (etc), when restore, dont read images/spectra - rather use the file as archive.
• note with images etc... held by scandata object - if the object is deleted, we can delete the images from the archive file. if the file is empty, delete the file.
• Also need an 'archive' option. (zip archive)
  • add and remove files
  • auto add files when update (ie monitor a directory and auto add files)

  • does normal 'open' work on files in zip? or should use FileOpen class??

  • The 'reader' class should deal with these archives... ie build a 'reader_archive' then ask the reader to read a file from the archive and give back a scan data object (or group of scan data objects as a data_group).

modules/xray/xrf

• work on xrf_plot (and med plot)
• error bars for xrf data / peaks
• use background.background in xrf
• note no reason to opt bgr params....
• speed up fits (use different lsq - see scipy.optimize lots of options)

modules/xray/xrd

• Structure Factor calcs
• CTR calcs

modules/xray/xrr

in compiled code

• Output penetration depth
• Note include thin film and transmission cell modes

python calcs

• Add routine that will step through theta and build matrix of I, etc, for plotting. i.e. make 3D plot like matlab code
• Fitting interface models, linking paramters, fit mult data sets etc...

modules/xray/xtab

• Interface for f',f'' and mu's 

modules/xtal

• gonio calcs - more geometries... and calc angles given constraints...
• lsq optimize of lattice params (and axis offsets)
• dictionary of space groups from international tables
• dictionary of transforms from international tables
• plane groups
• etc....
• read cif files.