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### OptimizeTemplateManager configuration example ###
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# An example YAML configuration to modify.
# Call `OptimizeTemplateManager.from_yaml(path)` to load this configuration.
particle_stack:
  df_path: results/results_goodModel.csv  # Needs to be readable by pandas
  extracted_box_size: [528, 528]
  original_template_size: [512, 512]
pixel_size_coarse_search:
  enabled: true
  pixel_size_min: -0.05
  pixel_size_max: 0.05
  pixel_size_step: 0.01
pixel_size_fine_search:
  enabled: true
  pixel_size_min: -0.005
  pixel_size_max: 0.005
  pixel_size_step: 0.001
preprocessing_filters:
  whitening_filter:
    do_power_spectrum: true
    enabled: true
    max_freq: 0.5  # In terms of Nyquist frequency
    num_freq_bins: null
  bandpass_filter:
    enabled: false
    falloff: null
    high_freq_cutoff: null
    low_freq_cutoff: null
computational_config:
  gpu_ids: 0
  num_cpus: 1
simulator:
  simulator_config:
    voltage: 300.0
    apply_dose_weighting: true
    dose_start: 0.0
    dose_end: 50.0
    dose_filter_modify_signal: "rel_diff"
    upsampling: -1  
    mtf_reference: "falcon4EC_300kv"
  pdb_filepath: "parsed_6Q8Y_whole_LSU_match3.pdb"
  volume_shape: [512, 512, 512]
  b_factor_scaling: 0.5
  additional_b_factor: 0
  pixel_spacing: 0.95