The calibration Module#

This module contains classes and functions that are used to calibrate detector data frames (i.e., to apply corrections for artifacts caused by the design and operation of the detector, not by any specific experimental condition).

class Agipd1MCalibration(calibration_filename: str, cellid_list: List[int])#

Bases: object

Calibration of the AGIPD 1M detector.

This class stores the calibration parameters for an AGIPD 1M detector and applies the calibration to a detector data frame upon request. Since the the full set of correction parameters for the AGIPD 1M detector takes up a lot of memory, only the parameters needed to correct frames originating from a subset of cells are loaded and stored. The subset of cells is chosen when the class is instantiated, via the cellid_list parameter. It will then be possible to apply the correction only on detector frames originating from the chosen set of cells.

Parameters:

calibration_filename (str) –
the absolute or relative path to an HDF5 file with the calibration parameters. The following data blocks should be present in the file:
- /AnalogOffset: a data block storing the offset coefficients for all pixels, cells and gain stages.
- /DigitalGainLevel: a data block storing the information needed to determine the gain state of each pixel and cell.
- /RelativeGain: a data block storing the gain coefficients for all pixels, cells and gain stages.
- /DetectorMask: a data block storing a mask that should be applied to each data frame. The pixels in the mask must have a value of either 0, meaning that the corresponding pixel in the data frame should be set to 0, or 1, meaning that the value of the corresponding pixel must be left alone.
The /AnalogOffset, /DigitalGainLevel, /RelativeGain data blocks must have an internal structure organized according to the following axis layout:
- axis 0: the three gain stages
- axis 1: the cell number
- axis 2: the ss coordinate of the 16 detector modules, seen as one big surface, stacked from module 0 to 15 along the longest edge, with the shortest edges touching.
- axis 3: the fs coordinate of the 16 detector modules, seen as one big surface, stacked from module 0 to 15 along the longest edge with the shortest edges touching.
cellid_list (Tuple[int]) – the list of cells for which the correction parameters should be loaded and stored.

apply_calibration(data_and_calibration_info: Dict[str, Any]) → Tuple[Any]#

Applies the calibration to a detector data frame.

This function determines the gain stage of each pixel in the data frame, and applies the relevant gain and offset corrections.

Parameters:

(Dict[str (data_and_calibration_info) –
a dictionary containing the data frame to calibrate, and some additional necessary information. The dictionary should contain the following entries:
- An entry with key ‘data’, whose value is the detector data frame to calibrate.
- An entry with key ‘info’, whose value is a nested dictionary with the following keys:
  - A key called ‘gain’ whose value is a numpy array of the same shape as the data frame to calibrate. Each pixel in this array must contain the information needed to determine the gain stage of the corresponding pixel in the data frame.
  - A key called ‘cell’, whose value is the cell number from which the frame to calibrate originates.
Any] –
a dictionary containing the data frame to calibrate, and some additional necessary information. The dictionary should contain the following entries:
- An entry with key ‘data’, whose value is the detector data frame to calibrate.
- An entry with key ‘info’, whose value is a nested dictionary with the following keys:
  - A key called ‘gain’ whose value is a numpy array of the same shape as the data frame to calibrate. Each pixel in this array must contain the information needed to determine the gain stage of the corresponding pixel in the data frame.
  - A key called ‘cell’, whose value is the cell number from which the frame to calibrate originates.

Returns:

the corrected data frame.

Return type:

numpy.ndarray