example_config_reconstruction.yml

analysis_name: RUBY_SWEEP_0 # 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:

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

material:
  definitions: materials.cpl
  active: ruby

image_series:
  file:
    stem: raw_data/RUBY_%04d # can include relative or absolute path
    ids: [4537, 4538] # or can use globs: ["*2[4-9]"]
  images:
    start: 2
  omega:
    start: -60.0
    step: 0.25
    stop: 60.0
  dark: RUBY_4537_medianDark
  flip: v # ~, v, h, hv, vh, cw, ccw

instrument:
  parameters: example_calibration.yml
  detector: # this section is only needed to convert old files to the new spec
    parameters_old: ge_ceo2.par # the old detector spec, produced by the GUI
    pixels: # this section required to convert from old detector spec
      rows: 2048
      columns: 2048
      size: [0.200, 0.200] # [row height, col width] mm

find_orientations:
  orientation_maps:
    # A file name must be specified. If it doesn't exist, one will be created
    file: RUBY_4537-4538_t15_eta-omega.cpl

    threshold: 15
    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
  #use_quaternion_grid: some/file/name # 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: 1.0 # degrees, defaults to ome tolerance

  threshold: 1 # defaults to 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 ["image_series:omega:start", "image_series:omega:start"+-360]
    ## depending on sign of "image_series:omega:step"
    #period: [-180, 180] # in degrees, defaults to full 360 starting at "ome start"

  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:
    radius: 1.0
    completeness: 0.51 # completeness threshold
    #algorithm: fclusterdata # defaults to dbscan

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

  estimate: RUBY_SWEEP_0/grains.out # defaults to None

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

  panel_buffer: 10 # don't fit spots within this many pixels from edge

  threshold: 25

  tolerance:
    tth: [0.25, 0.086] # tolerance lists must be identical length
    eta: [2.0, 0.75]
    omega: [1.0, 0.25]

  tth_max: 14.75 # true, false, or a non-negative value, defaults to true

---

analysis_name: RUBY_SWEEP_1 # defaults to analysis

image_series:
  file:
    ids: [4539, 4540] # or can use globs: ["*2[4-9]"]

---

analysis_name: RUBY_SWEEP_2 # defaults to analysis

image_series:
  file:
    ids: [4541, 4542] # or can use globs: ["*2[4-9]"]