Functioning HEDM workflow via CLI

Overview

This release has a functioning CLI for ff-HEDM data reduction. Recent fixes also affect line position extraction from powder diffraction data. A sample config file for the HEDM workflow is given below. Mac OS and Linux conda packages are available here.

This also incorporates the nf-HEDM utils from CHESS (see this paper.)

Example ff-HEDM config

This is a sample YAML file that is taken from the new hexrd examples repo.

analysis_name: results_hexrd06_py27  # defaults to analysis

# working directory defaults to current working directory
# all relative paths specified herein are assumed to be in the working_dir
# any files not in working_dir should be specified with an absolute path
#
# working_dir:

# "all", "half", or -1 means all but one, defaults to -1
multiprocessing: all 

material:
  definitions: materials_py27.hexrd
  active: ruby

image_series:
  format: frame-cache
  data:
    - file: ../imageseries/mruby-0129_000004_ff1_000012-cachefile.npz
      args: {}
      panel: ff1  # must match detector key
    - file: ../imageseries/mruby-0129_000004_ff2_000012-cachefile.npz
      args: {}
      panel: ff2  # must match detector key

instrument: dexelas_id3a_20200130.yml

find_orientations:
  orientation_maps:
    # A file name must be specified. If it doesn't exist, one will be created
    file: null

    threshold: 250
    bin_frames: 1 # defaults to 1

    # "all", or a list of hkl orders used to find orientations
    # defaults to all orders listed in the material definition
    active_hkls: [0,1,2,3,4,5]

  # either search full quaternion grid, or seed search based on sparse
  # orientation maps.  For input search space:
  #
  # use_quaternion_grid: some/file/name
  # 
  # otherwise defaults to seeded search:
  seed_search: # this section is ignored if use_quaternion_grid is defined
    hkl_seeds: [0,1,2] # hkls ids to use, must be defined for seeded search
    fiber_step: 0.5 # degrees, defaults to ome tolerance
    # Method selection:
    #   Now 3 choices: label (the original), 'blob_dog', and 'blob_log'
    #   Each has its own parameter names, examples below.
    #
    # method: 
    #   label: 
    #     filter_radius: 1
    #     threshold: 1 # defaults to 1
    #
    # method:
    #   blob_dog:
    #     min_sigma: 0.5
    #     max_sigma: 5
    #     sigma_ratio: 1.6
    #     threshold: 0.01
    #     overlap: 0.1
    #
    method:
      blob_log:
        min_sigma: 0.5
        max_sigma: 5
        num_sigma: 10
        threshold: 0.01
        overlap: 0.1
  # this is the on-map threshold using in the scoring
  # defaults to 1
  threshold: 1
   
  omega:
    tolerance: 1.0  # in degrees, defaults to 2x ome step

    # specify the branch cut, in degrees. The range must be 360 degrees.
    # defaults to full 360 starting at the first omega value in imageseries.
    period: [0, 360]

  eta:
    tolerance: 1.0  # in degrees, defaults to 2x ome step
    mask: 5  # degrees, mask angles close to ome rotation axis, defaults to 5

  clustering:
    # algorithm choices are 
    #   sph-dbscan
    #   ort-dbscn
    #   dbscan <default>
    #   fclusterdata; this is a fallback and won't work for large problems
    radius: 1.0
    completeness: 0.85 # completeness threshold
    algorithm: dbscan  

fit_grains:
  do_fit: true # if false, extracts grains but doesn't fit. defaults to true

  # estimate: null

  npdiv: 4 # number of polar pixel grid subdivisions, defaults to 2

  panel_buffer: 2 # don't fit spots within this many mm from edge

  threshold: 25

  tolerance:
    tth: [0.25, 0.20] # tolerance lists must be identical length
    eta: [3.0, 2.0]
    omega: [2.0, 1.0]

  refit: [2, 1]

  tth_max: false # true, false, or a non-negative value, defaults to true

Functioning HEDM workflow via CLI

This release now has a functioning CLI for the HEDM workflow, which consists of
-indexing (hexrd find-orientations)
-grain parameter refinement (hexrd fit-grains)
The preliminary tests against the examples in the examples repos passed; however, more verification is warranted.

Updates to calibration parameter handling.

This release adds the ability to calibrate a (multipanel) instrument from a list of grains. A few other fixes as well. This is likely one of the last releases on the py27 repo and will be used to generate "ground truth" data for continuous integration later.

Updates to wxPython 4

This release adds compatibility with the latest wxPython "Phoenix" release, which is the default in the anaconda and conda-forge channels.

Added blob finding to fiber generation

Along with some minor cleanup, now the fiber generation utilized blob finding by default. Config options remain hard-coded for now; testing is required. The settings worked well for the dexela CMOS detectors at CHESS as of February 2020.

Note that to build with miniconda3 (or anaconda3), you need to specify python 2 using the flag --python=2.7

Minor bug fix to eta-ome map generation

This release fixes a bug where for instances of incomplete rings containing the eta branch cut.

Minor bug fix

Import error when changing helper function to use transforms_CAPI.unitRowVector() to replace the call to matrixutil.unitVector(). Also cleared pylint warnings in instrument.py.

Improvements to HDF5 imageseries load

This branch is the same used for processing AFRL PUP August 2019 experiment, with an additional improvement in imageseries reading performance for HDF5 format.

Migrate to wxPython version 4; update build

As wxPython version 3 is no longer supported, this branch has been updated to be compatible with wxPython version 4 (chichis now the default version of the package for conda-build). Also updated the recipe and build document.

small bug fix

Latest release for multi panel indexing, fitting, and powder ring extraction.