Detector correction, geometry & spatial reduction

Steps that clean up detector frames, straighten a tilted dispersion axis, and collapse the spatial axes into a spectrum. See the step reference overview for the shape vocabulary and the read/write model.

Correction

common_mode_correction

Subtract a per-row, per-column, or per-bank baseline estimated from a signal-free band. Shape preserved.

• Reads: detector on — 3D (shots, rows, cols) or 2D (rows, cols).
• Writes: overwrites on; same shape.
• Parameters:

name	default	description
on	required	detector key
axis	"row"	row (per-row offset across columns), column, or bank
method	"median"	median (robust) or mean
reference	full extent	[start, end] of the dark band, indexed on the axis orthogonal to axis
bank_size	128	column width of an ePix100 bank; only used when axis: bank

The reference range is a column range for axis: row and a row range for axis: column or axis: bank.

- step: common_mode_correction
  on: epix
  axis: row
  reference: [0, 40]   # dark columns

patch_pixels

Repair bad pixels or columns, either from an explicit list or auto-detected.

• Reads: detector on — 1D, 2D, or 3D.
• Writes: overwrites on; same shape.
• Parameters:

name	default	description
on	required	detector key
pixels	None	explicit list of indices/columns to patch
auto_detect	False	find bad columns from the data instead of a list
threshold	5.0	auto-detect: deviation cut for flagging a column
nsigma	5.0	auto-detect: sigma multiplier for the flag
max_gap_width	4	widest run of bad pixels to bridge
smooth_window	31	window for the smoothed reference profile
mode	"polynomial"	polynomial, interpolate, or zero
axis	last	axis to patch along
patch_range	4	half-width of the neighborhood sampled around a bad pixel
poly_range	6	half-width of the fit window
deg	1	polynomial degree for mode: polynomial

- step: patch_pixels
  on: epix
  pixels: [383, 384]   # dead column pair
  mode: polynomial

Geometry

find_rotation_angle

Auto-detect the tilt of a dispersed signal so rotate_detector can straighten it.

• Reads: detector on — 3D (shots, rows, cols) or 2D.
• Writes: <on>_angle (override with angle_key) — float degrees.
• Parameters:

name	default	description
on	required	detector key
low_threshold	30	lower ADU bound for edge detection
high_threshold	100	upper ADU bound for edge detection
angle_key	<on>_angle	attribute to store the detected angle

- step: find_rotation_angle
  on: epix
  angle_key: epix_angle

rotate_detector

Rotate detector frames by a fixed angle or by a previously detected one.

• Reads: detector on — 3D or 2D.
• Writes: overwrites on.
• Parameters:

name	default	description
on	required	detector key
angle	0	rotation in degrees
angle_key	None	read the angle from this attribute; takes precedence over angle
axes	[1, 2] 3D / [0, 1] 2D	plane to rotate in
reshape	False	grow the output to fit the rotated frame vs keep shape

- step: find_rotation_angle
  on: epix
  angle_key: epix_angle
- step: rotate_detector
  on: epix
  angle_key: epix_angle

Spatial reduction

apply_roi

Crop to one or more regions of interest, keeping the spatial dimension.

• Reads: detector on — 2D or 3D.
• Writes: <on>_ROI_n (one per ROI, or combined) — spatial axes retained.
• Parameters:

name	default	description
on	required	detector key
rois	required	list of [row0, row1, col0, col1] crops
combine_rois	True	merge ROIs into one array vs keep separate _ROI_n

- step: apply_roi
  on: epix
  rois: [[270, 330, 400, 700]]

reduce_detector_spatial

Crop to ROIs and collapse one spatial axis into a per-shot dispersion trace.

• Reads: detector on — 3D (shots, rows, cols) or 2D.
• Writes: <on>_ROI_n — reduced along the chosen axis.
• Parameters:

name	default	description
on	required	detector key
rois	required	list of [row0, row1, col0, col1] crops
combine_rois	True	merge ROIs vs keep separate
reduction	"sum"	sum or mean over the reduced axis
axis	1 (3D) / -1	spatial axis to collapse
purge	True	drop the source key after reducing to free memory

ROI rows are given in absolute detector coordinates; the step translates them into the loaded crop using the run's _row_offset, so the same YAML works whether the detector was cropped at load or not.

- step: reduce_detector_spatial
  on: epix
  rois: [[270, 330, 400, 700]]
  reduction: sum

reduce_detector_shots

Collapse the shot axis into a single averaged or summed frame.

• Reads: detector on — shot axis is axis 0.
• Writes: <on>_reduced — shot axis removed.
• Parameters:

name	default	description
on	required	detector key
reduction	"sum"	sum or mean over shots
purge	True	drop the source key after reducing

- step: reduce_detector_shots
  on: epix
  reduction: mean