diff --git a/src/toolbox_scs/routines/boz.py b/src/toolbox_scs/routines/boz.py
index e5ac8d409cdedb4626860badab4f8ca0f3db0bad..aaeb08de8c7a1294ad2c89d937ab1f69f5190e9c 100644
--- a/src/toolbox_scs/routines/boz.py
+++ b/src/toolbox_scs/routines/boz.py
@@ -267,6 +267,34 @@ def _get_pixel_pos(module):
# keeping only module 15 pixel X,Y position
return g.get_pixel_positions()[module][:, :, :2]
+def get_roi_pixel_pos(roi, params):
+ """Compute fake or real pixel position of an roi from roi center.
+
+ Inputs:
+ -------
+ roi: dictionnary
+ params: parameters
+
+ Returns:
+ --------
+ X, Y: 1-d array of pixel position.
+ """
+ if params.use_hex:
+ # DSSC pixel position on hexagonal lattice
+ X = params.pixel_pos[roi['yl']:roi['yh'], roi['xl']:roi['xh'], 0]
+ Y = params.pixel_pos[roi['yl']:roi['yh'], roi['xl']:roi['xh'], 1]
+ else:
+ nY, nX = roi['yh'] - roi['yl'], roi['xh'] - roi['xl']
+ X = np.arange(nX)/100
+ Y = np.arange(nY)[:, np.newaxis]/100
+
+ # center of ROI is put to 0,0
+ X -= np.mean(X)
+ Y -= np.mean(Y)
+
+ return X, Y
+
+
def _get_pixel_corners(module):
"""Compute the pixel corners of DSSC module."""
# module pixel position
@@ -671,7 +699,7 @@ def inspect_rois(data_mean, rois, threshold=None, allrois=False):
# Flat field related functions
-def _plane_flat_field(p, roi, pixel_pos, use_hex=False):
+def _plane_flat_field(p, roi, params):
"""Compute the p plane over the given roi.
Given the plane parameters p, compute the plane over the roi
@@ -682,9 +710,7 @@ def _plane_flat_field(p, roi, pixel_pos, use_hex=False):
p: a vector of a, b, c, d plane parameter with the
plane given by ax+ by + cz + d = 0
roi: a dictionnary roi['yh', 'yl', 'xh', 'xl']
- pixel_pos: array of DSSC pixel position on hexagonal lattice
- use_hex: boolean, use actual DSSC pixel position from pixel_pos
- or fake cartesian pixel position
+ params: parameters
Returns
-------
@@ -693,19 +719,7 @@ def _plane_flat_field(p, roi, pixel_pos, use_hex=False):
"""
a, b, c, d = p
- if use_hex:
- # DSSC pixel position on hexagonal lattice
- pos = pixel_pos[roi['yl']:roi['yh'], roi['xl']:roi['xh'], :]
- X = pos[:, :, 0]
- Y = pos[:, :, 1]
- else:
- nY, nX = roi['yh'] - roi['yl'], roi['xh'] - roi['xl']
- X = np.arange(nX)/100
- Y = np.arange(nY)[:, np.newaxis]/100
-
- # center of ROI is put to 0,0
- X -= np.mean(X)
- Y -= np.mean(Y)
+ X, Y = get_roi_pixel_pos(roi, params)
Z = -(a*X + b*Y + d)/c
@@ -729,22 +743,20 @@ def compute_flat_field_correction(rois, params, plot=False):
flat_field = np.ones((128, 512))
plane = params.get_flat_field()
- use_hex = params.use_hex
- pixel_pos = params.pixel_pos
force_mirror = params.force_mirror
r = rois['n']
flat_field[r['yl']:r['yh'], r['xl']:r['xh']] = \
- _plane_flat_field(plane[:4], r, pixel_pos, use_hex)
+ _plane_flat_field(plane[:4], r, params)
r = rois['p']
if force_mirror:
a, b, c, d = plane[:4]
flat_field[r['yl']:r['yh'], r['xl']:r['xh']] = \
- _plane_flat_field([-a, b, c, d], r, pixel_pos, use_hex)
+ _plane_flat_field([-a, b, c, d], r, params)
else:
flat_field[r['yl']:r['yh'], r['xl']:r['xh']] = \
- _plane_flat_field(plane[4:], r, pixel_pos, use_hex)
+ _plane_flat_field(plane[4:], r, params)
if plot:
f, ax = plt.subplots(1, 1, figsize=(6, 2))
@@ -916,15 +928,17 @@ def plane_fitting_domain(avg, rois, prod_th, ratio_th):
"""
centers = {}
- for k, r in enumerate(['n', '0', 'p']):
- centers[r] = np.array([(rois[r]['yl'] + rois[r]['yh'])//2,
- (rois[r]['xl'] + rois[r]['xh'])//2])
+ for k in ['n', '0', 'p']:
+ r = rois[k]
+ centers[k] = np.array([(r['yl'] + r['yh'])//2,
+ (r['xl'] + r['xh'])//2])
k = 'n'
- num = avg[rois[k]['yl']:rois[k]['yh'], rois[k]['xl']:rois[k]['xh']]
+ r = rois[k]
+ num = avg[r['yl']:r['yh'], r['xl']:r['xh']]
d = '0'
denom = np.roll(avg, tuple(centers[k] - centers[d]))[
- rois[k]['yl']:rois[k]['yh'], rois[k]['xl']:rois[k]['xh']]
+ r['yl']:r['yh'], r['xl']:r['xh']]
n = num/denom
prod = num*denom
n_m = ((prod > prod_th[0]) * (prod < prod_th[1]) *
@@ -933,10 +947,11 @@ def plane_fitting_domain(avg, rois, prod_th, ratio_th):
n[~np.isfinite(n)] = 0
k = 'p'
- num = avg[rois[k]['yl']:rois[k]['yh'], rois[k]['xl']:rois[k]['xh']]
+ r = rois[k]
+ num = avg[r['yl']:r['yh'], r['xl']:r['xh']]
d = '0'
denom = np.roll(avg, tuple(centers[k] - centers[d]))[
- rois[k]['yl']:rois[k]['yh'], rois[k]['xl']:rois[k]['xh']]
+ r['yl']:r['yh'], r['xl']:r['xh']]
p = num/denom
prod = num*denom
p_m = ((prod > prod_th[0]) * (prod < prod_th[1]) *
@@ -984,39 +999,13 @@ def plane_fitting(params):
num_n = a_n**2 + b_n**2 + c_n**2
roi = params.rois['n']
- if params.use_hex:
- # DSSC pixel position on hexagonal lattice
- pos = params.pixel_pos[roi['yl']:roi['yh'], roi['xl']:roi['xh'], :]
- X = pos[:, :, 0]
- Y = pos[:, :, 1]
- else:
- nY, nX = n.shape
- X = np.arange(nX)/100
- Y = np.arange(nY)[:, np.newaxis]/100
-
- # center of ROI is put to 0,0
- X -= np.mean(X)
- Y -= np.mean(Y)
-
+ X, Y = get_roi_pixel_pos(roi, params)
d0_2 = np.sum(n_m*(a_n*X + b_n*Y + c_n*n + d_n)**2)/num_n
num_p = a_p**2 + b_p**2 + c_p**2
roi = params.rois['p']
- if params.use_hex:
- # DSSC pixel position on hexagonal lattice
- pos = params.pixel_pos[roi['yl']:roi['yh'], roi['xl']:roi['xh'], :]
- X = pos[:, :, 0]
- Y = pos[:, :, 1]
- else:
- nY, nX = p.shape
- X = np.arange(nX)/100
- Y = np.arange(nY)[:, np.newaxis]/100
-
- # center of ROI is put to 0,0
- X -= np.mean(X)
- Y -= np.mean(Y)
-
+ X, Y = get_roi_pixel_pos(roi, params)
if params.force_mirror:
d2_2 = np.sum(p_m*(-a_n*X + b_n*Y + c_n*p + d_n)**2)/num_n
else: