sample.yaml

# ==========================================================================
# ctapipe-process configuration file.
# version: 0.19.2
#
# This configuration contains a subset of options needed for a basic analysis.
# Not all possible options are shown. To get a complete list, run:
#
#     `ctapipe-process --help-all`
#
# ==========================================================================
Contact:  
  # please fill in your contact information here. It will be stored in the
  # output files as provenance information
  name: Miguel-Escobar
  email: mescob11@ucsc.edu
  organization: UCSC

DataWriter:
  # options that control what is stored in the output file by default here we
  # write nothing (can be overridden on the command-line or in subsequent config
  # files)
  overwrite: True # do not overwrite existing files
  write_images: False # store DL1 images
  write_parameters: True # store DL1 parameters
  write_showers: True # store DL2 stereo geometry
  write_raw_waveforms: False # write R0 waveforms
  write_waveforms: False # write R1 waveforms
  write_muon_parameters: False # analyze and write muon parameters

# options that specify the amount of information stored in log file.
Tool:
  log_file_level: 'INFO'
  log_level: 30

SimTelEventSource:
  focal_length_choice: 'EQUIVALENT'

# The CameraCalibrator takes data from R1 or DL0 to DL1a level, applying finer
# calibration and turning waveforms into images. It is run only if DL1a images
# do not already exist in the input file.
CameraCalibrator:
  # Choose an extractor type from the following possibilities:
  #'FullWaveformSum', 'FixedWindowSum', 'GlobalPeakWindowSum',
  #'LocalPeakWindowSum', 'SlidingWindowMaxSum', 'NeighborPeakWindowSum',
  #'TwoPassWindowSum', 'BaselineSubtractedNeighborPeakWindowSum'
  #
  # Note this is a telescope-wise parameter, so can be specified per telescope
  # if necessary (see below for an example)
  image_extractor_type:
    - ['type', 'MST*SCTCam', NeighborPeakWindowSum]
  #  - ['type', '*FlashCam', 'FlashCamExtractor']


# The ImageProcessor performs the DL1a-> DL1b (image parameters) transition. It
# is run only if the parameters `DataWriter.write_image_parameters=True` and the
# parameters don't already exist in the input file (or if the user forces them
# to be re-computed using DataWriter.recompute_dl1=True)
ImageProcessor:
  # The image cleaner selects pixels which have signal in them and rejects those
  # without. Options are: 'TailcutsImageCleaner', 'MARSImageCleaner',
  # 'FACTImageCleaner'
  
  # Write image parameters in telescope frame. 
  use_telescope_frame: True

  image_cleaner_type: TailcutsImageCleaner

  # make sure you include a configuration for the image cleaner you selected
  # above here. The section named by the image_cleaner_type will be used to
  # configure it.
  TailcutsImageCleaner:
    # the thresholds for this image cleaner must be optimized for the data set
    # you are analyzing. The defaults may not be correct and should be optimized
    # for the given use case.
    #
    # These are telescope-wise parameters, where the options are patterns
    # specified in a list in order of precedence, with later options overwriting
    # earlier ones. Each pattern is a triplet of [scope, key, value], where the
    # scope can be "type" (matching to the telescope type name) or "id"
    # (matching a specific telescope ID number). In the case of "type", the key
    # should be either a telescope type string, or part of one with "*" used as
    # a wildcard match (e.g. "LST*" would match all LST telescopes). You can
    # specify a universal default value using "*" as a key. Note that specifying
    # a single value is equivalent to specifying a one-item list containing
    # [type, '*', value] .
    picture_threshold_pe: # top-level threshold in photoelectrons
    #   - [type, "LST*", 8.5]
    #  - [type, "MST*NectarCam", 9.0]
    #  - [type, "MST*FlashCam", 9.0]
    #  - [type, "SST_ASTRI_CHEC", 4.0]
      - [type, "MST*SCTCam", 3.5]   
    boundary_threshold_pe: # second-level threshold in photoelectrons
    #  - [type, "LST*", 4.25]
    #  - [type, "MST*NectarCam", 4.5]
    #  - [type, "MST*FlashCam", 4.5]
    #  - [type, "SST_ASTRI_CHEC", 2.0]
      - [type,"MST*SCTCam", 1.5]
    keep_isolated_pixels: False # If False, pixels with  < min_picture_neighbors are removed.
    min_picture_neighbors: 2 # Minimum number of neighbors above threshold to consider

  # Choose which images should be parameterized:
  ImageQualityQuery:
    # quality critieria should be a list of pairs of [name, filter_expression]
    # The filter expression should contain the variable `image` which is the
    # image itself, a 1D np.array.
    quality_criteria:
      - ["enough_pixels", "np.count_nonzero(image) > 3"]
      - ["enough_charge", "image.sum() > 3"]


# The ShowerProcessor performs the DL1 to DL2a (reconstructed shower geometry)
# transition. It is run only if the parameter DataWriter.write_showers=True.
ShowerProcessor:
  # choose between HillasReconstructor and HillasIntersection or both (two
  # implementations of the standard stereo line-intersection method)
  reconstructor_types:
    - HillasReconstructor
      #  - HillasIntersection

  HillasReconstructor:
    # Choose which telescope events should be included in the reconstruction.
    StereoQualityQuery:
      # the quality criteria here should again be a list of [name,
      # filter_expression] pairs, filter_expression contains the variable
      # `parameters` which is a `ctapipe.containers.ImageParametersContainer`
      # for the current event
      quality_criteria:
        - ["enough_intensity", "parameters.hillas.intensity > 5"]
        - ["Positive_width", "parameters.hillas.width.value > 0"]
        - ["enough_pixels", "parameters.morphology.n_pixels > 3"]
        - ["centroid_to_center_of_camera_distance", "parameters.hillas.r.value < 4.5"]
        - ["not_clipped", "parameters.leakage.intensity_width_2 < 0.5"]

# The MuonProcessor analyses DL1 images for muons and writes muon parameters.
# It is only run if DataWriter.write_muon_parameters=True.
MuonProcessor:
  # Choose which events should be considered for muon analysis
  ImageParameterQuery:
    # quality critieria should be a list of pairs of [name, filter_expression]
    # The filter expression should contain the variable `dl1_params` which are the
    # image parameters.
    quality_criteria:
      - ["min_pixels", "dl1_params.morphology.n_pixels > 100"]
      - ["min_intensity", "dl1_params.hillas.intensity > 500"]

  # Choose which rings should be processed to the actual muon parameters
  RingQuery:
    # quality critieria should be a list of pairs of [name, filter_expression]
    # The filter expression can either contain the variable `parameters` 
    # (muon ring parameters like containment), `ring` (muon ring position and radius) 
    # or `mask` (pixel mask masking the rings pixels)
    quality_criteria:
      - ["radius_not_nan", "np.isfinite(ring.radius.value)"]
      - ["min_pixels", "np.count_nonzero(mask) > 50"]
      - ["ring_containment", "parameters.containment > 0.5"]