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added a way to select spots close to a 2theta-xbet region
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@BM32ESRF
BM32ESRF committed Jun 12, 2023
1 parent 558567c commit 14806a8
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Showing 5 changed files with 78 additions and 26 deletions.
2 changes: 1 addition & 1 deletion LaueTools/GUI/DetectorCalibration.py
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Expand Up @@ -2871,7 +2871,7 @@ def simulate_theo(self, removeharmonics=0):
Simulate theoretical Laue spots properties
removeharmonics: 1 keep only lowest hkl (fondamental) for each harmonics spots family
:param removeharmonics: 1 keep only lowest hkl (fondamental) for each harmonics spots family
0 consider all spots (fond. + harmonics)
return:
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2 changes: 1 addition & 1 deletion LaueTools/GUI/SimulFrame.py
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Original file line number Diff line number Diff line change
Expand Up @@ -837,7 +837,7 @@ def _replot(self):
else:
kwords["c"] = tuple(colors[grainindex])

print('np.array(self.Data_X[grainindex])',np.array(self.Data_X[grainindex]))
#print('np.array(self.Data_X[grainindex])',np.array(self.Data_X[grainindex]))

# theo Laue spots scatter plot
self.axes.scatter(np.array(self.Data_X[grainindex]) - self.X_offset,
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79 changes: 64 additions & 15 deletions LaueTools/lauecore.py
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Original file line number Diff line number Diff line change
Expand Up @@ -342,7 +342,7 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE
* [3](str): key for material element
:param kf_direction: string defining the average geometry, mean value of exit scattered vector:
'Z>0' top spots
'Z>0' top spots (at around 90 deg in 2theta scattering angles)
'Y>0' one side spots (towards hutch door)
Expand Down Expand Up @@ -380,6 +380,8 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE
(where dd vector is the smallest vector joining sample impact point and points on CCD plane)
y is perpendicular to x and z
.. note:: USED MultigrainSimulator.py (from polygrainsimulator Board)
"""
if isinstance(wavelmin, (float, int)) and isinstance(wavelmax, (float, int)):
if wavelmin < wavelmax and wavelmin > 0:
Expand Down Expand Up @@ -482,6 +484,7 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE

Orientmatrix = np.array(Orientmatrix)

# Q vectors
listrotvec = np.dot(Orientmatrix, np.dot(Bmatrix, table_vec.T))

listrotvec_X = listrotvec[0]
Expand All @@ -505,8 +508,9 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE
listObj = list

# Kf direction selection

# top reflection 2theta = 90
if kf_direction == "Z>0":
if kf_direction == "Z>0": # assuming that detector plane small enough and too much tilted, such as not potentially intersect Z<0 components
KF_condit = listrotvec_Z > 0.0
# side reflection 2theta = 90
elif kf_direction == "Y>0":
Expand All @@ -532,10 +536,10 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE
if len(kf_direction) != 2:
raise ValueError("kf_direction must be defined by a list of two angles !")
else:
kf_2theta, kf_chi = kf_direction
kf_2theta, kf_chi = kf_2theta * DEG, kf_chi * DEG
kf_2theta, kf_chi = kf_direction # in degree
kf_2theta, kf_chi = kf_2theta * DEG, kf_chi * DEG # now in radians

qmean_theta, qmean_chi = kf_2theta / 2.0, kf_chi
qmean_theta, qmean_chi = kf_2theta / 2.0, kf_chi # in radian

print("central q angles", qmean_theta, qmean_chi)

Expand Down Expand Up @@ -572,8 +576,8 @@ def getLaueSpots(wavelmin, wavelmax, crystalsParams, kf_direction=DEFAULT_TOP_GE
((listrotvec_X * 2.0 / wlm + arraysquare) <= 0.0),
((listrotvec_X * 2.0 / wlM + arraysquare) > 0.0),
), (KF_condit))
# print "nb of spots in spheres and in towards CCD region", len(np.where(Condit == True)[0])

# q vectors and Miller indices are calculated
if fastcompute == 0:
# print 'Using detailled computation mode'

Expand Down Expand Up @@ -896,7 +900,8 @@ def create_spot_back(pos_vec, miller, detectordistance, allattributes=False,

return spotty

def filterQandHKLvectors(vec_and_indices, detectordistance, detectordiameter, kf_direction='Z>0'):
def filterQandHKLvectors(vec_and_indices, detectordistance, detectordiameter,
kf_direction='Z>0', shiftcentercamera=None):
"""filter vector Q and HKL in vec_and_indices
:param vec_and_indices: arrays of vectors Q and HKL
Expand All @@ -907,10 +912,13 @@ def filterQandHKLvectors(vec_and_indices, detectordistance, detectordiameter, kf
:type detectordiameter: float
:param kf_direction: geometry of detection label or two angles giving 2theta chi direction of detector, defaults to 'Z>0'
:type kf_direction: str or 2 floats, optional
: param shiftcentercamera: Default is None, xbet angle in degree to shift significantly the center of collected Laue spots from basic position defined by kf_direction
:raises ValueError: [description]
:raises ValueError: [description]
:return: [oncam_vec], [oncam_HKL]
:rtype: [np.array of 3 elements, np.array of 3 elements]
.. note:: Xcam and Ycam in mm (not in pixel unit!)
"""
Qvectors_list, HKLs_list = vec_and_indices
Qx = Qvectors_list[0][:, 0] * 1.0
Expand All @@ -929,7 +937,17 @@ def filterQandHKLvectors(vec_and_indices, detectordistance, detectordiameter, kf
# Kf direction selection
if kf_direction == "Z>0": # top reflection geometry
ratiod = detectordistance / Qz
Ycam = ratiod * (Qx + Rewald)
if shiftcentercamera is not None:
#Ycam = ratiod * (Qx + Rewald) - detectordistance*np.tan(shiftcentercamera*DEG)
#Ycam = ratiod * (Qx - np.tan(shiftcentercamera*DEG/2.)*Qz+ Rewald)

#theta = np.arctan(Qx/Qz)/DEG
myxbet = (np.pi/2 + 2.*np.arctan(Qx/Qz))/DEG
# print('Qx', np.amin(Qx), np.mean(Qx), np.amax(Qx))
# print('mygam', np.amin(myxbet), np.mean(myxbet), np.amax(myxbet))
Ycam = -detectordistance*np.tan(shiftcentercamera*DEG-myxbet*DEG)
else: # Qx is negative
Ycam = ratiod * (Qx + Rewald)
Xcam = ratiod * (Qy)
elif kf_direction == "Y>0": # side reflection geometry (for detector between the GMT hutch door and the sample (beam coming from right to left)
ratiod = detectordistance / Qy
Expand Down Expand Up @@ -975,7 +993,12 @@ def filterQandHKLvectors(vec_and_indices, detectordistance, detectordiameter, kf
oncam_Qy = np.compress(onCam_cond, Qy)
oncam_Qz = np.compress(onCam_cond, Qz)

myxbet_oncam = (np.pi/2 + 2.*np.arctan(oncam_Qx/oncam_Qz))/DEG
#print('myxbet_oncam', np.amin(myxbet_oncam), np.mean(myxbet_oncam), np.amax(myxbet_oncam))
mytheta_oncam = np.arctan(oncam_Qx/oncam_Qz)/DEG
#print('mytheta_oncam', np.amin(mytheta_oncam), np.mean(mytheta_oncam), np.amax(mytheta_oncam))
oncam_vec = np.array([oncam_Qx, oncam_Qy, oncam_Qz]).T
#print('len(oncam_vec)',len(oncam_vec))

oncam_H = np.compress(onCam_cond, indi_H)
oncam_K = np.compress(onCam_cond, indi_K)
Expand All @@ -994,7 +1017,8 @@ def filterLaueSpots(vec_and_indices, HarmonicsRemoval=1,
pixelsize=165.0 / 2048,
dim=(2048, 2048),
linestowrite=[[""]],
verbose=0):
verbose=0,
shiftcentercamera=None):
r""" Calculates list of grains spots on camera and without harmonics
and on CCD camera from [[spots grain 0],[spots grain 1],etc] =>
returns [[spots grain 0],[spots grain 1],etc] w / o harmonics and on camera CCD
Expand Down Expand Up @@ -1071,7 +1095,17 @@ def filterLaueSpots(vec_and_indices, HarmonicsRemoval=1,
# Kf direction selection
if kf_direction == "Z>0": # top reflection geometry
ratiod = detectordistance / Qz
Ycam = ratiod * (Qx + Rewald)
if shiftcentercamera is not None:
#Ycam = ratiod * (Qx + Rewald) - detectordistance*np.tan(shiftcentercamera*DEG)
#Ycam = ratiod * (Qx - np.tan(shiftcentercamera*DEG/2.)*Qz+ Rewald)

#theta = np.arctan(Qx/Qz)/DEG
myxbet = (np.pi/2 + 2.*np.arctan(Qx/Qz))/DEG
# print('Qx', np.amin(Qx), np.mean(Qx), np.amax(Qx))
# print('mygam', np.amin(myxbet), np.mean(myxbet), np.amax(myxbet))
Ycam = -detectordistance*np.tan(shiftcentercamera*DEG-myxbet*DEG)
else: # Qx is negative
Ycam = ratiod * (Qx + Rewald)
Xcam = ratiod * (Qy)
elif kf_direction == "Y>0": # side reflection geometry (for detector between the GMT hutch door and the sample (beam coming from right to left)
ratiod = detectordistance / Qy
Expand Down Expand Up @@ -1226,7 +1260,8 @@ def filterLaueSpots_full_np(veccoord, indicemiller, onlyXYZ=False, HarmonicsRemo
detectordiameter=DEFAULT_DETECTOR_DIAMETER,
pixelsize=165.0 / 2048,
dim=(2048, 2048),
grainindex=0):
grainindex=0,
shiftcentercamera=None):
r""" Calculates spots data for an individual grain
on camera and without harmonics
and on CCD camera
Expand All @@ -1248,6 +1283,8 @@ def filterLaueSpots_full_np(veccoord, indicemiller, onlyXYZ=False, HarmonicsRemo
the incoming beam and sample)
:type kf_direction: string
:param shiftcentercamera: default None, angular value of xbet angle (from detector calibration parameters to center scattered beams around the center of the camera)
:return: tuple of lists of Twtheta Chi Energy Millers if fastcompute=0
tuple of lists 2theta, chi if fastcompute=1
Expand All @@ -1270,7 +1307,15 @@ def filterLaueSpots_full_np(veccoord, indicemiller, onlyXYZ=False, HarmonicsRemo
if kf_direction == "Z>0": # top reflection geometry
# VecZ is >0
ratiod = detectordistance / VecZ
Ycam = ratiod * (VecX + Rewald)
if shiftcentercamera is not None:
#Ycam = ratiod * (Qx + Rewald) - detectordistance*np.tan(shiftcentercamera*DEG)
#Ycam = ratiod * (Qx - np.tan(shiftcentercamera*DEG/2.)*Qz+ Rewald)

myxbet = np.pi/2 + 2.*np.arctan(VecX/VecZ)

Ycam = - detectordistance * np.tan(shiftcentercamera*DEG - myxbet)
else: # VecX is negative
Ycam = ratiod * (VecX + Rewald)
Xcam = ratiod * (VecY)
elif kf_direction == "Y>0": # side reflection geometry (for detector between the GMT hutch door and the sample (beam coming from right to left)
ratiod = detectordistance / VecY
Expand Down Expand Up @@ -1327,6 +1372,8 @@ def filterLaueSpots_full_np(veccoord, indicemiller, onlyXYZ=False, HarmonicsRemo
oncam_vecY = np.compress(onCam_cond, VecY)
oncam_vecZ = np.compress(onCam_cond, VecZ)

#print('nb of laue spots after filtering',len(oncam_vecZ))

if onlyXYZ:
return np.array([oncam_vecX, oncam_vecY, oncam_vecZ]).T

Expand Down Expand Up @@ -1357,7 +1404,7 @@ def filterLaueSpots_full_np(veccoord, indicemiller, onlyXYZ=False, HarmonicsRemo
dim=dim,
kf_direction=kf_direction)

# print 'TwthetaChiEnergy_list_one_grain', TwthetaChiEnergy_list_one_grain
# print 'TwthetaChiEnergy_list_one_grain', TwthetaChiEnergy_list_one_grain
# Creating list of spot with or without harmonics
if HarmonicsRemoval and True: # listspot:
raise ValueError("Harmonic removal is not implemented and listspot does not exist anymore")
Expand Down Expand Up @@ -1904,7 +1951,8 @@ def SimulateLaue_full_np(grain, emin, emax,detectorparameters,
detectordiameter=DETECTORDIAMETER,
kf_direction=kf_direction,
HarmonicsRemoval=0,
pixelsize=pixelsize)
pixelsize=pixelsize,
shiftcentercamera=detectorparameters[3])

Twicetheta_zerodepth, Chi_zerodepth, Energy, Miller_ind = TwthetaChiEnergyMillers_list_one_grain_wo_harmonics[:4]

Expand Down Expand Up @@ -2088,6 +2136,7 @@ def simulatepurepattern_np(grain, emin, emax, kf_direction, data_filename, PlotL
fastcompute=0,
kf_direction=kf_direction,
detectordistance=detectordistance,
HarmonicsRemoval=HarmonicsRemoval)
HarmonicsRemoval=HarmonicsRemoval,
correctcenterfromxbet=None) # could be xbet value

return True
9 changes: 6 additions & 3 deletions LaueTools/matchingrate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -705,7 +705,8 @@ def Angular_residues_np(test_Matrix, twicetheta_data, chi_data, ang_tol=0.5,
detectordistance=detectordistance,
detectordiameter=detectordiameter,
pixelsize=pixelsize,
dim=dim)
dim=dim,
correctcenterfromxbet=None)

# old calculation with spots instantiation
# TwicethetaChi = LAUE.filterLaueSpots(spots2pi, fileOK=0, fastcompute=1,
Expand All @@ -732,7 +733,8 @@ def Angular_residues_np(test_Matrix, twicetheta_data, chi_data, ang_tol=0.5,
detectordistance=detectordistance,
detectordiameter=detectordiameter,
pixelsize=pixelsize,
dim=dim)
dim=dim,
correctcenterfromxbet=None)

# Y should be Q vectors corresponding to exp. twicetheta_data and chi_data
Y = LaueGeo.from_twchi_to_q((twicetheta_data, chi_data)).T
Expand Down Expand Up @@ -810,7 +812,8 @@ def Angular_residues_np_multimatrices(ListMatrices, twicetheta_data, chi_data, a
detectordistance=detectordistance,
detectordiameter=detectordiameter,
pixelsize=pixelsize,
dim=dim)
dim=dim,
correctcenterfromxbet=None)
# print("matindex",matindex)
Arr_Theo2Theta[matindex] = TheoTwicethetaChi[0][:NBMAXPEAKS]
Arr_TheoChi[matindex] = TheoTwicethetaChi[1][:NBMAXPEAKS]
Expand Down
12 changes: 6 additions & 6 deletions LaueTools/multigrainsSimulator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,7 @@ def dosimulation_parametric(_list_param, Transform_params=None, SelectGrains=Non
print("GrainSimulParam in dosimulation_parametric() input Element")
print(GrainSimulParam)

# q vectors in lauetools frame + miller indices
spots2pi = LAUE.getLaueSpots(DictLT.CST_ENERGYKEV / emax,
DictLT.CST_ENERGYKEV / emin,
[GrainSimulParam], # bracket because of a list of one grain
Expand All @@ -218,15 +219,13 @@ def dosimulation_parametric(_list_param, Transform_params=None, SelectGrains=Non
kf_direction=kf_direction,
dictmaterials=dictmaterials)

# q vectors in lauetools frame, miller indices
# print "spots2pi",spots2pi

# --------- [list of 3D vectors],[list of corresponding Miller indices]

# remove Parent Grain Laue spots too close from detector border vicinity
Qvectors_ParentGrain, HKLs_ParentGrain = LAUE.filterQandHKLvectors(spots2pi,
detectordistance,
detectordiameter, kf_direction)
detectordistance,
detectordiameter, kf_direction,
shiftcentercamera=cameraAngles[0])

# Qvectors_ParentGrain, HKLs_ParentGrain = spots2pi

Expand Down Expand Up @@ -431,7 +430,8 @@ def dosimulation_parametric(_list_param, Transform_params=None, SelectGrains=Non
detectordiameter=detectordiameter*1.2, # * 1.2, # avoid losing some spots in large transformation
kf_direction=kf_direction,
HarmonicsRemoval=1,
pixelsize=pixelsize)
pixelsize=pixelsize,
shiftcentercamera=cameraAngles[0])

# for elem in Laue_spot_list[0][:10]:
# print elem
Expand Down

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