Pixel masks

Cheetah includes a mask in its output identifying the status of each pixel. This can be thought of as extended bad pixel mask containing more information about the state of each pixel, some of which is calculated ‘on the fly’ by Cheetah itself.

The current mask definition is given below.

Some of the fields are obvious, and some of them are very specific to some applications (in particular single particle imaging). We may revise these fields at some point in time.

Current mask definition

* Bits for pixel masks

* Oriented along conventions defined for CXI file format ( https://github.com/FilipeMaia/CXI/raw/master/cxi_file_format.pdf )

* CONVENTIONS:

* - All options are dominantly inherited during assembly and pixel integration (see assembleImage.cpp)

* - The default value for all options is "false"

static const uint16_t PIXEL_IS_PERFECT = 0; // Remember to change this value if necessary after adding a new option

static const uint16_t PIXEL_IS_INVALID = 1; // bit 0

static const uint16_t PIXEL_IS_SATURATED = 2; // bit 1

static const uint16_t PIXEL_IS_HOT = 4; // bit 2

static const uint16_t PIXEL_IS_DEAD = 8; // bit 3

static const uint16_t PIXEL_IS_SHADOWED = 16; // bit 4

static const uint16_t PIXEL_IS_IN_PEAKMASK = 32; // bit 5

static const uint16_t PIXEL_IS_TO_BE_IGNORED = 64; // bit 6

static const uint16_t PIXEL_IS_BAD = 128; // bit 7

static const uint16_t PIXEL_IS_OUT_OF_RESOLUTION_LIMITS = 256; // bit 8

static const uint16_t PIXEL_IS_MISSING = 512; // bit 9

static const uint16_t PIXEL_IS_NOISY = 1024; // bit 10

static const uint16_t PIXEL_IS_ARTIFACT_CORRECTED = 2048; // bit 11

static const uint16_t PIXEL_FAILED_ARTIFACT_CORRECTION = 4096; // bit 12

static const uint16_t PIXEL_IS_PEAK_FOR_HITFINDER = 8192; // bit 13

static const uint16_t PIXEL_IS_PHOTON_BACKGROUND_CORRECTED = 16384; // bit 14

static const uint16_t PIXEL_IS_IN_JET = 32768;// bit 15