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### MatchTemplateManager configuration example ###
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# An example YAML configuration to modify.
# Call `MatchTemplateManager.from_yaml(path)` to load this configuration.
template_volume_path: /some/path/to/template.mrc
micrograph_path:      /some/path/to/micrograph.mrc
match_template_result:
  allow_file_overwrite: true
  mip_path:                   /some/path/to/output_mip.mrc
  scaled_mip_path:            /some/path/to/output_scaled_mip.mrc
  orientation_psi_path:       /some/path/to/output_orientation_psi.mrc
  orientation_theta_path:     /some/path/to/output_orientation_theta.mrc
  orientation_phi_path:       /some/path/to/output_orientation_phi.mrc
  relative_defocus_path:      /some/path/to/output_relative_defocus.mrc
  correlation_average_path:   /some/path/to/output_correlation_average.mrc
  correlation_variance_path:  /some/path/to/output_correlation_variance.mrc
optics_group:
  label: some_label
  voltage: 300.0
  pixel_size: 1.06   # in Angstroms
  defocus_u: 5200.0  # in Angstroms
  defocus_v: 4950.0  # in Angstroms
  astigmatism_angle: 25.0  # in degrees
  spherical_aberration: 2.7  # in millimeters
  amplitude_contrast_ratio: 0.07
  phase_shift: 0.0
  ctf_B_factor: 60.0  # in Angstroms^2
defocus_search_config:
  defocus_max:  1200.0  # in Angstroms, relative to the defocus_u and defocus_v values
  defocus_min: -1200.0  # in Angstroms, relative to the defocus_u and defocus_v values
  defocus_step: 200.0   # in Angstroms
  enabled: true
orientation_search_config:
  base_grid_method: uniform
  psi_step: 1.5      # in degrees
  theta_step: 2.5  # in degrees
preprocessing_filters:
  whitening_filter:
    enabled: true
    do_power_spectrum: true
    max_freq: 0.5  # In terms of Nyquist frequency
    num_freq_bins: null
  bandpass_filter:
    enabled: false
    falloff: null
    high_freq_cutoff: null  # Both in terms of Nyquist frequency (e.g. low-pass to 3 Å @ 1.06 Å/px would be high_freq_cutoff=0.353)
    low_freq_cutoff: null
computational_config:
  gpu_ids:
  - 0
  num_cpus: 1