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XFELPP

impl

impl

Section titled “impl”

Classes

Section titled “Classes”
Name Description
PF8Peak_v1 An identified peak within an image including associated metadata.
RadialStatistics A wrapping container for buffers needed to compute radial background statistics.

Functions

Section titled “Functions”
Return Name Description
void compute_radial_background Compute the statistics to determine background signal in radial segments.
void compute_local_background_ring Compute the background signal locally around a peak candidate.
void integrate_peak_intensity Integrate a finalized peak candidate and write it to the output buffer.
void ccl_peak_search Run the connected-components labelling and peak integration on an image.

compute_radial_background

Section titled “compute_radial_background”
void compute_radial_background(const float * data, const float * r_map, const bool * mask, RadialStatistics & rstats, std::size_t num_pixels, int niter = 5, float ADC_threshold = 10.0f, float min_SNR = 7.0f)

Compute the statistics to determine background signal in radial segments.

Parameters

Section titled “Parameters”
Parameter Type Description
data const float * The image data.
r_map const float * The radius map for computing radial bins.
mask const bool * The validity mask for each pixel in the image.
rstats [RadialStatistics](api-xalgospp-features-impl-RadialStatistics.md#radialstatistics) & The output where background radial statistics are stored.
num_pixels std::size_t The total number of pixels in the image (and mask, etc.).
ADC_threshold float The cut-off for the pixel intensity.
min_SNR float The minimum signal to noise ratio to use.

compute_local_background_ring

Section titled “compute_local_background_ring”
void compute_local_background_ring(const float * data, const float * r_map, const bool * mask, float peak_com_fs, float peak_com_ss, int width, int height, std::vector< std::uint8_t > & pix_in_peak_map, float & bg_sum, float & bg_sum_sq, float & bg_max_i, int & bg_count, RadialStatistics & rstats, int local_background_radius)

Compute the background signal locally around a peak candidate.

Parameters

Section titled “Parameters”
Parameter Type Description
data const float * The image data.
r_map const float * The radius map for computing radial bins.
mask const bool * The validity mask for each pixel in the image.
peak_com_fs float The center of mass of the candidate in the fast-scan axis.
peak_com_ss float The center of mass of the candidate in the slow-scan axis.
width int The width of the image (fast-scan axis).
height int The height of the image (slow-scan axis).
pix_in_peak_map std::vector< std::uint8_t > & Registry holding pixels in each candidate peak.
bg_sum float & The output local background intensity sum.
bg_sum_sq float & The output local background intensity sum squared.
bg_max_i float & The output local background maximum pixel intensity.
bg_count int & The output number of pixels in the local background.
rstats [RadialStatistics](api-xalgospp-features-impl-RadialStatistics.md#radialstatistics) & The pre-computed radial statistics for the GLOBAL background.
local_background_radius int The radius to use for the local background.

integrate_peak_intensity

Section titled “integrate_peak_intensity”
void integrate_peak_intensity(const float * data, int width, int height, int num_pix_in_peak, int com_idx, PF8Peak_v1 * peak_list_out, int & peak_count, std::vector< int > & peak_pixels, float local_offset, float local_sigma, float bg_max_i, int max_number_peaks, long max_pixel_count, float min_SNR)

Integrate a finalized peak candidate and write it to the output buffer.

Parameters

Section titled “Parameters”
Parameter Type Description
data const float * The image data.
width int The width of the image (fast-scan axis).
height int The height of the image (slow-scan axis).
num_pix_in_peak int The total number of pixels in the candidate peak.
com_idx int The linearized pixel index for the peak center.
peak_list_out [PF8Peak_v1](api-xalgospp-features-impl-PF8Peak_v1.md#pf8peak_v1) * The output buffer to write integrated peaks.
peak_count int & The output counter for the total number of peaks found so far.
peak_pixels std::vector< int > & The pixels in the peak.
local_offset float The local background mean offset.
local_sigma float The local background standard deviation.
bg_max_i float The local background maximum pixel intensity.
max_number_peaks int The maximum number of peaks to find.
max_pixel_count long The maximum number of pixels to allow in a peak.
min_SNR float The minimum signal-to-noise ratio to allow for a peak.

Section titled “ccl_peak_search”
void ccl_peak_search(const float * data, const float * r_map, const bool * mask, PF8Peak_v1 * peak_list_out, int & num_peaks_out, RadialStatistics & rstats, std::vector< std::uint8_t > & pix_in_peak_map, std::vector< int > & infs, std::vector< int > & inss, std::vector< int > & peak_pixels, int width, int height, long min_pixel_count, long max_pixel_count, int local_background_radius, int max_number_peaks, float min_SNR = 7.0f)

Run the connected-components labelling and peak integration on an image.

Parameters

Section titled “Parameters”
Parameter Type Description
data const float * The image data.
r_map const float * The radius map for computing radial bins.
mask const bool * The validity mask for each pixel in the image.
peak_list_out [PF8Peak_v1](api-xalgospp-features-impl-PF8Peak_v1.md#pf8peak_v1) * The output buffer to write integrated peaks.
num_peaks_out int & The finalized count of peaks found.
rstats [RadialStatistics](api-xalgospp-features-impl-RadialStatistics.md#radialstatistics) & The pre-computed radial statistics for the GLOBAL background.
pix_in_peak_map std::vector< std::uint8_t > & Registry holding pixels in each candidate peak.
infs std::vector< int > & Buffer for tracking peak pixels in the fast-scan axis.
inss std::vector< int > & Buffer for tracking peak pixels in the slow-scan axis.
peak_pixels std::vector< int > & The pixels in the peak.
width int The width of the image (fast-scan axis).
height int The height of the image (slow-scan axis).
min_pixel_count long The minimum number of pixels to allow in a peak.
max_pixel_count long The maximum number of pixels to allow in a peak.
local_background_radius int The radius, around a peak candidate, to use for the local background calculations.
max_number_peaks int The maximum number of peaks to find.
min_SNR float The minimum peak candidate signal-to-noise ratio to allow.