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Genome Damage and Stability Centre SMLM Package Software for single molecule localisation microscopy (SMLM)
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syntax = "proto3";

// ProtoBuffer description file for configuration settings of the GDSC SMLM Java code.
// Authors: Alex Herbert, 2017
// License: GPL V3
package uk.ac.sussex.gdsc.smlm.data.config;

option java_outer_classname = "CalibrationProtos";

import "uk/ac/sussex/gdsc/smlm/data/config/unit.proto";
import "uk/ac/sussex/gdsc/smlm/data/config/fit.proto";

// Define the calibration for distance
message DistanceCalibration {
  // The distance unit.
  DistanceUnit distance_unit = 1;
  // The camera pixel size in nanometers.
  double nm_per_pixel = 2;
}

// Define the calibration for time
message TimeCalibration {
  // The time unit. This is currently unused as it is assumed the time in the results
  // is in frames.
  TimeUnit time_unit = 1;
  // The exposure time in milliseconds per frame.
  double exposure_time = 2;
}

message IntensityCalibration {
  // The intensity unit.
  IntensityUnit intensity_unit = 1;
  // The gain (Count/photon). Can be used to convert the signal in Analogue-to-Digital
  // count units (Counts) to photons.
  double count_per_photon = 2;
}

// Define the calibration for angles
message AngleCalibration {
  // The angle units, e.g. for a rotated point spread function.
  AngleUnit angle_unit = 1;
}

// The camera type
enum CameraType {
  CAMERA_TYPE_NA = 0; // Not available
  EMCCD = 1; // Electron Multiplying Charge Coupled Device (EM CCD)
  CCD = 2; // Charge Coupled Device (CCD)
  SCMOS = 3; // Scientific Complementary Metal-Oxide-Semiconductor (sCMOS)
}

// Define the camera calibration
message CameraCalibration {
  // Amplification (count/electron) has been removed and replaced by quantum efficiency
  reserved 4;
  reserved "count_per_electron";

  // The camera type.
  CameraType camera_type = 1;

  // The camera Gaussian read noise (in Counts).
  double read_noise = 2;

  // The camera bias (in Counts)
  double bias = 3;

  // The camera model name. This should contain all the information required to
  // load the camera model, e.g. in the case of a per-pixel camera model for sCMOS cameras.
  string camera_model_name = 5;

  // Define the quantum efficiency (QE in electron/photon) of the microscope camera.
  // Note that the camera noise model assumes that photons are converted to counts by
  // a process that is not perfect (i.e. it has noise). The underlying process is
  // photons converted to electrons in the camera chip and then amplification
  // (count/electron) occurring in the camera hardware. Ideally this should be recorded
  // by storing the QE and the amplification. However the total gain (Count/photon)
  // is already stored with the results. Thus the amplification can be inferred by
  // dividing the total gain by the quantum efficiency which should be in the range 0-1.
  double quantum_efficiency = 6;
}

// Define the calibration for the result data
message ResultDataCalibration {
  // Results may have an XY localisation precision. This stores the method used to
  // compute the localisation precision.
  PrecisionMethod precision_method = 1;
}

// Define the calibration for the results. The calibration contains details of the
// results units and how to convert them. Note that data can be loaded without knowledge
// of the camera used so the distance, time and intensity calibration are separate.
message Calibration {
  // The distance calibration.
  DistanceCalibration distance_calibration = 1;

  // The time calibration.
  TimeCalibration time_calibration = 2;

  // The intensity calibration
  IntensityCalibration intensity_calibration = 3;

  // The angle calibration.
  AngleCalibration angle_calibration = 4;

  // The camera calibration.
  CameraCalibration camera_calibration = 5;

  // The result data calibration.
  ResultDataCalibration result_data_calibration = 6;
}

// Define a camera model resource that can be loaded
message CameraModelResource {
  // The x origin of the camera pixel data
  int32 x = 1;
  // The y origin of the camera pixel data
  int32 y = 2;
  // The width of the camera pixel data
  int32 width = 3;
  // The height of the camera pixel data
  int32 height = 4;
  // The filename where the model data is stored
  string filename = 5;
}

// Define the camera model settings
message CameraModelSettings {
  map camera_model_resources = 1;
}