{
  "title": "CamfiConfig",
  "description": "Camfi configuration.",
  "type": "object",
  "properties": {
    "root": {
      "title": "Root",
      "description": "Directory containing all images for the project.",
      "default": ".",
      "format": "directory-path",
      "type": "string"
    },
    "disable_progress_bar": {
      "title": "Disable Progress Bar",
      "description": "Disables progress bars. By default, disable on\n\nnon-TTY. To force the progress bar to appear, set\n\nthis to false.",
      "type": "boolean"
    },
    "via_project_file": {
      "title": "Via Project File",
      "description": "Path to file containing VIA project. Can either be\n\ngiven as a single path or a list of paths. If a\n\nlist is given, then the VIA projects will be\n\nmerged.",
      "anyOf": [
        {
          "type": "array",
          "items": {
            "type": "string",
            "format": "file-path"
          }
        },
        {
          "type": "string",
          "format": "file-path"
        }
      ]
    },
    "day_zero": {
      "title": "Day Zero",
      "description": "Used as reference date for plotting etc. Currently\n\nthe Camfi CLI does not access this value, However\n\nit is used in some of the example notebooks.",
      "type": "string",
      "format": "date"
    },
    "output_tz": {
      "title": "Timezone",
      "description": "Sets a global timezone to convert all timezones\n\nto, for simpler comparison between locations in\n\ndifferent timezones.",
      "pattern": "^Z|[+-]\\d{2}(?::?\\d{2})?$",
      "examples": [
        "Z",
        "+10:00",
        "-05"
      ],
      "type": "string"
    },
    "default_output": {
      "title": "Default Output",
      "description": "Path to write output. Outputs defined in\n\nwingbeat_extractor and annotator take precedence\n\nover this.",
      "type": "string",
      "format": "path"
    },
    "filters": {
      "$ref": "#/definitions/FilterConfig"
    },
    "camera": {
      "$ref": "#/definitions/CameraConfig"
    },
    "time": {
      "$ref": "#/definitions/LocationTimeCollector"
    },
    "place": {
      "$ref": "#/definitions/LocationWeatherStationCollector"
    },
    "wingbeat_extraction": {
      "$ref": "#/definitions/WingbeatExtractorConfig"
    },
    "annotator": {
      "$ref": "#/definitions/AnnotatorConfig"
    }
  },
  "definitions": {
    "ImageFilterConfig": {
      "title": "ImageFilterConfig",
      "description": "Contains options for filtering images from a VIA project.",
      "type": "object",
      "properties": {
        "min_annotations": {
          "title": "Min Annotations",
          "description": "Exclude images if they have fewer annotations than\n\nthis.",
          "type": "integer"
        },
        "exclude_images": {
          "title": "Exclude Images",
          "description": "Images to exclude from VIA project. Can either be\n\na list of paths to image files, or a single path\n\nto a text file (i.e. not a list). If the latter,\n\nimage file paths will be read from text file, one\n\nper line.",
          "type": "array",
          "items": {
            "type": "string",
            "format": "path"
          }
        },
        "include_images": {
          "title": "Include Images",
          "description": "Images to include from VIA project. Images not in\n\nthis list will be excluded. Can either be a list\n\nof paths to image files, or a single path to a\n\ntext file (i.e. not a list). If the latter, image\n\nfile paths will be read from text file, one per\n\nline.",
          "type": "array",
          "items": {
            "type": "string",
            "format": "path"
          }
        }
      }
    },
    "FloatFilter": {
      "title": "FloatFilter",
      "type": "object",
      "properties": {
        "ge": {
          "title": "Greater-than or Equal-to",
          "description": "Only include region if attribute >= this value.",
          "type": "number"
        },
        "le": {
          "title": "Less-than or Equal-to",
          "description": "Only include region if attribute <= this value.",
          "type": "number"
        },
        "exclude_none": {
          "title": "Exclude None",
          "description": "Whether to exclude region if attribute is not set.",
          "default": false,
          "type": "boolean"
        }
      },
      "required": [
        "ge",
        "le"
      ]
    },
    "RegionFilterConfig": {
      "title": "RegionFilterConfig",
      "type": "object",
      "properties": {
        "score": {
          "title": "Score",
          "description": "Sets filters for the score region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "best_peak": {
          "title": "Best Peak",
          "description": "Sets filters for the best_peak region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "blur_length": {
          "title": "Blur Length",
          "description": "Sets filters for the blur_length region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "snr": {
          "title": "Snr",
          "description": "Sets filters for the snr region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "wb_freq_up": {
          "title": "Wb Freq Up",
          "description": "Sets filters for the wb_freq_up region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "wb_freq_down": {
          "title": "Wb Freq Down",
          "description": "Sets filters for the wb_freq_down region\n\nattribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "et_up": {
          "title": "Et Up",
          "description": "Sets filters for the et_up region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        },
        "et_dn": {
          "title": "Et Dn",
          "description": "Sets filters for the et_dn region attribute.",
          "allOf": [
            {
              "$ref": "#/definitions/FloatFilter"
            }
          ]
        }
      },
      "description": "Contains options for filtering regions (annotations) from images, based on the values of region attributes. "
    },
    "FilterConfig": {
      "title": "FilterConfig",
      "description": "Contains settings for filtering images and/or regions (annotations) from a VIA\nproject.",
      "type": "object",
      "properties": {
        "image_filters": {
          "$ref": "#/definitions/ImageFilterConfig"
        },
        "region_filters": {
          "$ref": "#/definitions/RegionFilterConfig"
        }
      }
    },
    "CameraConfig": {
      "title": "CameraConfig",
      "description": "Camera hardware-related configuration.",
      "type": "object",
      "properties": {
        "camera_time_to_actual_time_ratio": {
          "title": "Camera Time To Actual Time Ratio",
          "description": "Used for correcting timestamps from an inaccurate\n\nclock. A value of 1.0 means the camera's clock\n\nruns at the correct speed. A value less than 1.0\n\nmeans that the camera's clock is slow, and a value\n\ngreater than 1.0 means the camera's clock is fast.",
          "type": "number"
        },
        "line_rate": {
          "title": "Line Rate",
          "description": "Rolling-shutter line rate of camera (lines per\n\nsecond). Used during wingbeat extraction to\n\ndetermine the effective exposure time for moving\n\nobjects (flying insects) in images. This is\n\nrequired in order to calculate wingbeat frequency\n\naccurately.",
          "exclusiveMinimum": 0,
          "type": "number"
        }
      }
    },
    "LocationTime": {
      "description": "Camera placement data",
      "type": "object",
      "properties": {
        "camera_start_time": {
          "title": "Camera Start Time",
          "description": "Camera placement datetime (according to camera's\n\nclock).",
          "type": "string",
          "format": "date-time"
        },
        "actual_start_time": {
          "title": "Actual Start Time",
          "description": "Actual camera placement datetime (defaults to\n\ncamera_start_time).",
          "type": "string",
          "format": "date-time"
        },
        "camera_end_time": {
          "title": "Camera End Time",
          "description": "Camera retrieval time (according to camera's\n\nclock).",
          "type": "string",
          "format": "date-time"
        },
        "actual_end_time": {
          "title": "Actual End Time",
          "description": "Actual camera retrieval time.",
          "type": "string",
          "format": "date-time"
        },
        "location": {
          "title": "Location",
          "description": "Name of location the camera was placed in.",
          "type": "string"
        }
      },
      "required": [
        "camera_start_time"
      ]
    },
    "LocationTimeCollector": {
      "title": "LocationTimeCollector",
      "description": "Contains data for multiple camera placements.",
      "type": "object",
      "properties": {
        "camera_placements": {
          "title": "Camera Placements",
          "description": "Mapping from sub-directories containing images to\n\nLocationTime instances.",
          "type": "object",
          "additionalProperties": {
            "$ref": "#/definitions/LocationTime"
          }
        }
      },
      "required": [
        "camera_placements"
      ]
    },
    "Location": {
      "title": "Location",
      "description": "Contains spatial data on locations, including timezone.",
      "type": "object",
      "properties": {
        "name": {
          "title": "Name",
          "description": "Name of location. Used to link to camera\n\nplacements.",
          "type": "string"
        },
        "lat": {
          "title": "Lat",
          "description": "Decimal latitude.",
          "type": "number"
        },
        "lon": {
          "title": "Lon",
          "description": "Decimal longitude.",
          "type": "number"
        },
        "elevation_m": {
          "title": "Elevation M",
          "description": "Elevation in metres.",
          "minimum": 0,
          "type": "number"
        },
        "tz": {
          "title": "Timezone",
          "description": "ISO8601 timezone offset.",
          "pattern": "^Z|[+-]\\d{2}(?::?\\d{2})?$",
          "examples": [
            "Z",
            "+10:00",
            "-05"
          ],
          "type": "string"
        }
      },
      "required": [
        "name",
        "lat",
        "lon",
        "elevation_m",
        "tz"
      ]
    },
    "WeatherStation": {
      "title": "WeatherStation",
      "description": "Contains information on a weather station.",
      "type": "object",
      "properties": {
        "location": {
          "title": "Location",
          "description": "Location of weather station.",
          "allOf": [
            {
              "$ref": "#/definitions/Location"
            }
          ]
        },
        "data_file": {
          "title": "Data File",
          "description": "Path to csv file containing weather data from\n\nweather station. The firt 6 lines of the file are\n\nskipped, and the 7th should contain column\n\nheaders. Should have one line per date. Minimally,\n\nthe first column should be date, in YYYY-mm-dd\n\nformat.",
          "format": "file-path",
          "type": "string"
        }
      },
      "required": [
        "location",
        "data_file"
      ]
    },
    "LocationWeatherStationCollector": {
      "title": "LocationWeatherStationCollector",
      "description": "Defines Locations and Weather stations.",
      "type": "object",
      "properties": {
        "locations": {
          "title": "Locations",
          "description": "list of locations where cameras have been placed.",
          "type": "array",
          "items": {
            "$ref": "#/definitions/Location"
          }
        },
        "weather_stations": {
          "title": "Weather Stations",
          "description": "list of weather stations.",
          "type": "array",
          "items": {
            "$ref": "#/definitions/WeatherStation"
          }
        },
        "location_weather_station_mapping": {
          "title": "Location Weather Station Mapping",
          "description": "A mapping between location names and\n\nweather_station names.",
          "type": "object",
          "additionalProperties": {
            "type": "string"
          }
        }
      },
      "required": [
        "locations",
        "weather_stations",
        "location_weather_station_mapping"
      ]
    },
    "WingbeatExtractorConfig": {
      "title": "WingbeatExtractorConfig",
      "description": "Contains configurable parameters for WingbeatExtractor.",
      "type": "object",
      "properties": {
        "device": {
          "title": "Device",
          "description": "Using GPU ('cuda') can give 4x speedups for\n\ncertain operations.",
          "default": "cpu",
          "type": "string"
        },
        "backup_device": {
          "title": "Backup Device",
          "description": "Used when computation fails on main device due to\n\nmemory limit.",
          "type": "string"
        },
        "scan_distance": {
          "title": "Scan Distance",
          "description": "Max. distance from polyline used for wingbeat\n\nextraction.",
          "default": 50,
          "exclusiveMinimum": 0,
          "type": "integer"
        },
        "max_pixel_period": {
          "title": "Max Pixel Period",
          "description": "Max. pixel period to check during wingbeat\n\nextraction.",
          "exclusiveMinimum": 0,
          "type": "integer"
        },
        "force_load_exif_metadata": {
          "title": "Force Load Exif Metadata",
          "description": "Forces EXIF metadata to be read from image instead\n\nof ViaProject.",
          "default": false,
          "type": "boolean"
        }
      }
    },
    "BoundingBox": {
      "title": "BoundingBox",
      "description": "Defines a bounding box with integer (pixel) coordinates.",
      "type": "object",
      "properties": {
        "x0": {
          "title": "X0",
          "description": "Minimum inclusive (horizontal) x-coordinate of\n\nbox.",
          "minimum": 0,
          "type": "integer"
        },
        "y0": {
          "title": "Y0",
          "description": "Minimum inclusive (vertical) y-coordinate of box.",
          "minimum": 0,
          "type": "integer"
        },
        "x1": {
          "title": "X1",
          "description": "Maximum exclusive (horizontal) x-coordinate of\n\nbox.",
          "minimum": 0,
          "type": "integer"
        },
        "y1": {
          "title": "Y1",
          "description": "Maximum exclusive (vertical) y-coordinate of box.",
          "minimum": 0,
          "type": "integer"
        }
      },
      "required": [
        "x0",
        "y0",
        "x1",
        "y1"
      ]
    },
    "MaskMaker": {
      "title": "MaskMaker",
      "description": "Contains settings for segmentation mask generation.",
      "type": "object",
      "properties": {
        "shape": {
          "title": "Shape",
          "description": "Shape of images (height, width) in pixels.",
          "type": "array",
          "items": [
            {
              "type": "integer",
              "exclusiveMinimum": 0
            },
            {
              "type": "integer",
              "exclusiveMinimum": 0
            }
          ]
        },
        "mask_dilate": {
          "title": "Mask Dilate",
          "description": "Morphological dilation to apply to segmentation\n\nskeletons.",
          "exclusiveMinimum": 0,
          "type": "integer"
        }
      },
      "required": [
        "shape"
      ]
    },
    "TrainingConfig": {
      "title": "TrainingConfig",
      "description": "Contains settings for camfi annotator model training.",
      "type": "object",
      "properties": {
        "mask_maker": {
          "$ref": "#/definitions/MaskMaker"
        },
        "min_annotations": {
          "title": "Min Annotations",
          "description": "Only train on images which have at least this many\n\nannotations. It often makes sense to set this to a\n\nlow number (e.g. 1). This will mean that any image\n\nwith *no* annotations in it will be skipped.",
          "type": "integer"
        },
        "max_annotations": {
          "title": "Max Annotations",
          "description": "Only train on images which have at most this many\n\nannotations. This option exists because GPU memory\n\nconsumption during each step of training depends\n\non the number of annotations in the loaded images,\n\nso images with a lot of annotations can cause\n\ntraining to crash. It probably makes sense to\n\nleave this unset, and only set it if you are\n\nrunnning into GPU memory errors.",
          "type": "integer"
        },
        "box_margin": {
          "title": "Box Margin",
          "description": "Margin (in pixels) to add to bounding boxes of\n\nobject annotations. This may affect endpoint\n\nestimation of polyline annotataions during\n\ninference.",
          "default": 10,
          "exclusiveMinimum": 0,
          "type": "integer"
        },
        "test_set_file": {
          "title": "Test Set File",
          "description": "Path to file containing filepaths (one per line).\n\nDo not set if test_set is set.",
          "format": "file-path",
          "type": "string"
        },
        "test_set": {
          "title": "Test Set",
          "description": "list of images to exclude from training. Also used\n\nby validator to determine which subsets of images\n\nto validate against.",
          "default": [],
          "type": "array",
          "items": {
            "type": "string",
            "format": "path"
          }
        },
        "load_pretrained_model": {
          "title": "Load Pretrained Model",
          "description": "Path or url to model .pth file or one of\n\ncamfi.models.model_urls to initialise training. By\n\ndefault, Resnet50 FPN backbone trained on the COCO\n\ndataset is used.",
          "examples": [
            "v1",
            "v2",
            "v2.1.4",
            "release"
          ],
          "anyOf": [
            {
              "type": "string",
              "format": "path"
            },
            {
              "type": "string"
            }
          ]
        },
        "device": {
          "title": "Device",
          "description": "Device to run training on. Use cuda for a Nvidia\n\nGPU.",
          "default": "cpu",
          "examples": [
            "cuda",
            "cpu"
          ],
          "type": "string"
        },
        "batch_size": {
          "title": "Batch Size",
          "description": "Number of images to load at once. This has memory\n\nconsumption implications, So if you're running in\n\nto problems with memory availability on the GPU,\n\nconsider lowering this.",
          "default": 5,
          "type": "integer"
        },
        "num_workers": {
          "title": "Num Workers",
          "description": "Number of worker processes for data loader to\n\nspawn. Depending on your machine, setting this\n\nreally high can have diminishing returns as system\n\nIO will become the rate-limiting step.",
          "default": 2,
          "type": "integer"
        },
        "num_epochs": {
          "title": "Num Epochs",
          "description": "Number of epochs (traversals of the entire\n\ntraining set) to train. Note that data\n\naugmentation (e.g. random horizontal flipping) is\n\napplied only once to each image during each epoch.",
          "default": 10,
          "type": "integer"
        },
        "outdir": {
          "title": "Outdir",
          "description": "Path to directory where to save model (or models\n\nif save_intermediate is set).",
          "default": ".",
          "format": "directory-path",
          "type": "string"
        },
        "model_name": {
          "title": "Model Name",
          "description": "Identifier to include in the file name of the\n\ntrained model(s). By default, this will be\n\ninferred from the date the configuration is\n\nparsed, in the format YYYYmmdd.",
          "type": "string"
        },
        "save_intermediate": {
          "title": "Save Intermediate",
          "description": "If True, model is saved after each epoch. By\n\ndefault, the model is only saved at the very end.",
          "default": false,
          "type": "boolean"
        }
      }
    },
    "InferenceConfig": {
      "title": "InferenceConfig",
      "description": "Contains settings for camfi annotator inference.",
      "type": "object",
      "properties": {
        "output_path": {
          "title": "Output Path",
          "description": "If set, automatically generated annotations will\n\nbe written to the file at the specified path. If\n\nunset, then the annotations will be written to the\n\nfile at the path specified by\n\nCamfiConfig.default_output. If neither is set, the\n\nannotations will not be written to file, which is\n\nprobably only useful if you are using camfi as a\n\npython module, rather than from the command line.",
          "type": "string",
          "format": "path"
        },
        "model": {
          "title": "Model",
          "description": "Pre-trained instance segmentation model to use\n\nduring automated annotaton. Can be a path or url\n\nto a model .pth file or one of\n\ncamfi.models.model_urls.",
          "default": "release",
          "examples": [
            "v1",
            "v2",
            "v2.1.4",
            "release"
          ],
          "anyOf": [
            {
              "type": "string",
              "format": "path"
            },
            {
              "type": "string"
            }
          ]
        },
        "device": {
          "title": "Device",
          "description": "Specifies device to run inference on.",
          "default": "cpu",
          "examples": [
            "cpu",
            "cuda"
          ],
          "type": "string"
        },
        "backup_device": {
          "title": "Backup Device",
          "description": "Used for images which fail on device due to memory\n\nconstraints. It is recommended to set this to\n\n'cpu' if device is set to 'cuda'.",
          "type": "string"
        },
        "split_angle": {
          "title": "Split Angle",
          "description": "Approximate maximum angle between polyline\n\nsegments in degrees.",
          "default": 15.0,
          "exclusiveMinimum": 0,
          "type": "number"
        },
        "poly_order": {
          "title": "Poly Order",
          "description": "Order of polynomial used for fitting motion blur\n\npaths.",
          "default": 2,
          "exclusiveMinimum": 0,
          "type": "integer"
        },
        "endpoint_method": {
          "title": "Endpoint Method",
          "description": "Method to find endpoints of motion blurs.",
          "default": "truncate",
          "examples": [
            "truncate"
          ],
          "type": "string"
        },
        "endpoint_extra_args": {
          "title": "Endpoint Extra Args",
          "description": "Extra arguments to pass to endpoint method\n\nfunction.",
          "default": [
            10
          ],
          "type": "array",
          "items": {}
        },
        "score_thresh": {
          "title": "Score Thresh",
          "description": "Score threshold between 0.0 and 1.0 for automatic\n\nannotations to be kept.Setting this to higher\n\nvalues will result fewer annotations being made.",
          "default": 0.0,
          "type": "number"
        },
        "overlap_thresh": {
          "title": "Overlap Thresh",
          "description": "Minimum weighted IoM between 0.0 and 1.0 for non-\n\nmaximum suppression of detections. Setting this to\n\nhigher values will result in a higher number of\n\nannotations being made, since fewer pairs of\n\nannotations will be assumed to relate to the same\n\nobject as eachother.",
          "default": 0.4,
          "type": "number"
        },
        "edge_thresh": {
          "title": "Edge Thresh",
          "description": "Polyline annotations which go this close (measured\n\nin pixels) to edge of the image will be converted\n\nto circle annotations. This is because wingbeat\n\nmeasurements cannot be made unless the entire\n\nmotion blur is contained within the image.",
          "default": 20,
          "minimum": 0,
          "type": "integer"
        }
      }
    },
    "ValidationConfig": {
      "title": "ValidationConfig",
      "description": "Contains settings for camfi annotator validation.",
      "type": "object",
      "properties": {
        "autoannotated_via_project_file": {
          "title": "Autoannotated Via Project File",
          "description": "Path to file containing VIA Project with\n\nautomatically obtained annotations to validate.",
          "type": "string",
          "format": "path"
        },
        "iou_thresh": {
          "title": "Iou Thresh",
          "description": "Threshold of bounding-box intersection-over-union\n\nto match automatically obtained annotations to\n\nground truth annotations.",
          "default": 0.5,
          "type": "number"
        },
        "image_sets": {
          "title": "Image Sets",
          "description": "Image sets to perform validation on. Possible sets\n\nare 'all', 'test', and 'train'. Multiple sets can\n\nbe specified. If including 'test' or 'train',\n\nannotator.training must also be configured.",
          "default": [
            "all"
          ],
          "pattern": "^(all|test|train)$",
          "type": "array",
          "items": {
            "type": "string",
            "pattern": "^(all|test|train)$"
          }
        },
        "output_dir": {
          "title": "Output Dir",
          "description": "If set, results of validation will be saved to\n\nthis directory (one file per image set).",
          "format": "directory-path",
          "type": "string"
        },
        "output_stem": {
          "title": "Output Stem",
          "description": "Stem of output files. Output files will be saved\n\nas ``output_dir/output_stem.image_set.json``.",
          "default": "validation",
          "type": "string"
        }
      }
    },
    "AnnotatorConfig": {
      "title": "AnnotatorConfig",
      "description": "Settings for automatic annotation training and inference.",
      "type": "object",
      "properties": {
        "crop": {
          "$ref": "#/definitions/BoundingBox"
        },
        "training": {
          "$ref": "#/definitions/TrainingConfig"
        },
        "inference": {
          "$ref": "#/definitions/InferenceConfig"
        },
        "validation": {
          "$ref": "#/definitions/ValidationConfig"
        }
      }
    }
  }
}