Indexation of spots data set.

Using Class spotsSet and play with spots considered for indexation and refinement

This Notebook is a part of Tutorials on LaueTools Suite. Author:J.-S. Micha Date: July 2019

%matplotlib inline

import matplotlib
import numpy as np
import matplotlib.pyplot as plt
import time,copy,os

# third party LaueTools import
import LaueTools.readmccd as RMCCD
import LaueTools.LaueGeometry as F2TC
import LaueTools.indexingSpotsSet as ISS
import LaueTools.IOLaueTools as RWASCII

/home/micha/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
  from ._conv import register_converters as _register_converters

module Image / PIL is not installed
LaueToolsProjectFolder /home/micha/LaueToolsPy3/LaueTools
Cython compiled module 'gaussian2D' for fast computation is not installed!
module Image / PIL is not installed
Entering CrystalParameters **---***********************


Cython compiled module for fast computation of Laue spots is not installed!
Cython compiled 'angulardist' module for fast computation of angular distance is not installed!
Using default module
Cython compiled module for fast computation of angular distance is not installed!
module Image / PIL is not installed

refinement from guessed solutions with two materials (see script IndexingTwinsSeries)

Let’s take a simple example of a single Laue Pattern. From the peak search we get 83 spots

folder= '../Examples/Ge/'
datfilename='Ge0001.dat'

key_material='Ge'
emin, emax= 5,23

# detector geometry and parameters as read from Ge0001.det
calibration_parameters = [69.179, 1050.81, 1115.59, 0.104, -0.273]
CCDCalibdict = {}
CCDCalibdict['CCDCalibParameters'] = calibration_parameters
CCDCalibdict['framedim'] = (2048, 2048)
CCDCalibdict['detectordiameter'] = 165.
CCDCalibdict['kf_direction'] = 'Z>0'
CCDCalibdict['xpixelsize'] = 0.08057
# CCDCalibdict can also be simply build by reading the proper .det file
print("reading geometry calibration file")
CCDCalibdict=RWASCII.readCalib_det_file(os.path.join(folder,'Ge0001.det'))
CCDCalibdict['kf_direction'] = 'Z>0'

reading geometry calibration file
calib =  [ 6.91790e+01  1.05081e+03  1.11559e+03  1.04000e-01 -2.73000e-01
  8.05700e-02  2.04800e+03  2.04800e+03]
matrix =  [-0.211596  0.092178 -0.973001 -0.77574   0.589743  0.224568  0.594521
  0.802313 -0.053281]

Compute scattering angles from spots pixel positions and detector geometry. Write a .cor file from .dat including these new infos

F2TC.convert2corfile(datfilename,
                         calibration_parameters,
                         dirname_in=folder,
                        dirname_out=folder,
                        CCDCalibdict=CCDCalibdict)
corfilename = datfilename.split('.')[0] + '.cor'
fullpathcorfile = os.path.join(folder,corfilename)

nb of spots and columns in .dat file (83, 3)
file :../Examples/Ge/Ge0001.dat
containing 83 peaks
(2theta chi X Y I) written in ../Examples/Ge/Ge0001.cor

Create an instance of the class spotset. Initialize spots properties to data contained in .cor file

DataSet = ISS.spotsset()

DataSet.importdatafromfile(fullpathcorfile)

CCDcalib in readfile_cor {'dd': 69.179, 'xcen': 1050.81, 'ycen': 1115.59, 'xbet': 0.104, 'xgam': -0.273, 'xpixelsize': 0.08057, 'ypixelsize': 0.08057, 'CCDLabel': 'sCMOS', 'framedim': [2048.0, 2048.0], 'detectordiameter': 165.00736, 'kf_direction': 'Z>0', 'pixelsize': 0.08057}
CCD Detector parameters read from .cor file
CCDcalibdict {'dd': 69.179, 'xcen': 1050.81, 'ycen': 1115.59, 'xbet': 0.104, 'xgam': -0.273, 'xpixelsize': 0.08057, 'ypixelsize': 0.08057, 'CCDLabel': 'sCMOS', 'framedim': [2048.0, 2048.0], 'detectordiameter': 165.00736, 'kf_direction': 'Z>0', 'pixelsize': 0.08057}

True

Class methods and attributes rely on a dictionnary of spots properties. key = exprimental spot index, val = spots properties

[DataSet.indexed_spots_dict[k] for k in range(10)]

[[0, 78.215821, 1.638153, 1027.11, 1293.28, 70931.27, 0],
 [1, 64.329767, -20.824155, 1379.17, 1553.58, 51933.84, 0],
 [2, 68.680451, -15.358122, 1288.11, 1460.16, 22795.07, 0],
 [3, 105.61498, 8.176187, 926.22, 872.06, 19489.69, 0],
 [4, 103.859791, 27.866566, 595.46, 876.44, 19058.79, 0],
 [5, 120.59561, -8.92066, 1183.27, 598.92, 17182.88, 0],
 [6, 60.359458, 26.483191, 626.12, 1661.28, 15825.39, 0],
 [7, 56.269853, 12.967153, 856.14, 1702.52, 15486.2, 0],
 [8, 82.072076, -35.89243, 1672.67, 1258.62, 13318.81, 0],
 [9, 83.349535, -27.458061, 1497.4, 1224.7, 13145.99, 0]]

DataSet.getUnIndexedSpotsallData()[:3]

array([[ 0.0000000e+00,  7.8215821e+01,  1.6381530e+00,  1.0271100e+03,
         1.2932800e+03,  7.0931270e+04],
       [ 1.0000000e+00,  6.4329767e+01, -2.0824155e+01,  1.3791700e+03,
         1.5535800e+03,  5.1933840e+04],
       [ 2.0000000e+00,  6.8680451e+01, -1.5358122e+01,  1.2881100e+03,
         1.4601600e+03,  2.2795070e+04]])

dict_loop = {'MATCHINGRATE_THRESHOLD_IAL': 100,
                   'MATCHINGRATE_ANGLE_TOL': 0.2,
                   'NBMAXPROBED': 6,
                   'central spots indices': [0,],
                   'AngleTolLUT': 0.5,
                   'UseIntensityWeights': False,
                   'nbSpotsToIndex':10000,
                   'list matching tol angles':[0.5,0.5,0.2,0.2],
                   'nlutmax':3,
                   'MinimumNumberMatches': 3,
                   'MinimumMatchingRate':3
                   }
grainindex=0
DataSet = ISS.spotsset()

DataSet.pixelsize = CCDCalibdict['xpixelsize']
DataSet.dim = CCDCalibdict['framedim']
DataSet.detectordiameter = CCDCalibdict['detectordiameter']
DataSet.kf_direction = CCDCalibdict['kf_direction']
DataSet.key_material = key_material
DataSet.emin = emin
DataSet.emax = emax

Normally we read all spots data from a .cor file

DataSet.importdatafromfile(fullpathcorfile)
DataSet.emin

CCDcalib in readfile_cor {'dd': 69.179, 'xcen': 1050.81, 'ycen': 1115.59, 'xbet': 0.104, 'xgam': -0.273, 'xpixelsize': 0.08057, 'ypixelsize': 0.08057, 'CCDLabel': 'sCMOS', 'framedim': [2048.0, 2048.0], 'detectordiameter': 165.00736, 'kf_direction': 'Z>0', 'pixelsize': 0.08057}
CCD Detector parameters read from .cor file
CCDcalibdict {'dd': 69.179, 'xcen': 1050.81, 'ycen': 1115.59, 'xbet': 0.104, 'xgam': -0.273, 'xpixelsize': 0.08057, 'ypixelsize': 0.08057, 'CCDLabel': 'sCMOS', 'framedim': [2048.0, 2048.0], 'detectordiameter': 165.00736, 'kf_direction': 'Z>0', 'pixelsize': 0.08057}

but we can import a custom list of spots. For example, starting from spots a the previous .cor file

Gespots = RWASCII.readfile_cor(fullpathcorfile)[0]

CCDcalib in readfile_cor {'dd': 69.179, 'xcen': 1050.81, 'ycen': 1115.59, 'xbet': 0.104, 'xgam': -0.273, 'xpixelsize': 0.08057, 'ypixelsize': 0.08057, 'CCDLabel': 'sCMOS', 'framedim': [2048.0, 2048.0], 'detectordiameter': 165.00736, 'kf_direction': 'Z>0', 'pixelsize': 0.08057}
CCD Detector parameters read from .cor file

# 2theta chi X, Y Intensity of the first 7 spots
Gespots[:7,:5]

array([[ 7.82158210e+01,  1.63815300e+00,  1.02711000e+03,
         1.29328000e+03,  7.09312700e+04],
       [ 6.43297670e+01, -2.08241550e+01,  1.37917000e+03,
         1.55358000e+03,  5.19338400e+04],
       [ 6.86804510e+01, -1.53581220e+01,  1.28811000e+03,
         1.46016000e+03,  2.27950700e+04],
       [ 1.05614980e+02,  8.17618700e+00,  9.26220000e+02,
         8.72060000e+02,  1.94896900e+04],
       [ 1.03859791e+02,  2.78665660e+01,  5.95460000e+02,
         8.76440000e+02,  1.90587900e+04],
       [ 1.20595610e+02, -8.92066000e+00,  1.18327000e+03,
         5.98920000e+02,  1.71828800e+04],
       [ 6.03594580e+01,  2.64831910e+01,  6.26120000e+02,
         1.66128000e+03,  1.58253900e+04]])

tth,chi,X,Y,I=Gespots[:,:5].T
exp_data_all=np.array([tth,chi,I,X,Y])
exp_data_all.shape

(5, 83)

#select some exp spots from absolute index   (6,0,2,30,9,8,20,10,5,1,7,14)
tth_e,chi_e,X_e,Y_e,I_e = (np.take(Gespots[:,:5],(6,0,2,30,9,8,20,10,5,1,7,14),axis=0)).T
exp_data=np.array([tth_e,chi_e,I_e,X_e,Y_e])

spots data must be imported as an array of 5 elements: 2theta, chi, Intensity, pixelX, pixelY

DataSet.importdata(exp_data)
DataSet.detectorparameters = calibration_parameters
DataSet.nbspots = len(exp_data[0])
DataSet.filename = 'short_'+corfilename
#DataSet.setSelectedExpSpotsData(0)
DataSet.getSelectedExpSpotsData(0)

(array([[ 6.03594580e+01,  7.82158210e+01,  6.86804510e+01,
          1.08452917e+02,  8.33495350e+01,  8.20720760e+01,
          8.17712570e+01,  9.17982210e+01,  1.20595610e+02,
          6.43297670e+01,  5.62698530e+01,  1.14942090e+02],
        [ 2.64831910e+01,  1.63815300e+00, -1.53581220e+01,
          3.77494610e+01, -2.74580610e+01, -3.58924300e+01,
          3.03824700e+01, -8.30994100e+00, -8.92066000e+00,
         -2.08241550e+01,  1.29671530e+01,  1.15295700e+01],
        [ 1.58253900e+04,  7.09312700e+04,  2.27950700e+04,
          4.40061000e+03,  1.31459900e+04,  1.33188100e+04,
          6.13787000e+03,  1.17999300e+04,  1.71828800e+04,
          5.19338400e+04,  1.54862000e+04,  1.00105200e+04]]),
 array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11]))

core function to index a set of spots

by defaut DataSet.getUnIndexedSpotsallData() is called

if use_file = 0, then current non indexed exp. spots will be considered for indexation

if use_file = 1, reimport data from file and reset also spots properties dictionary (i.e. with status unindexed)

DataSet.IndexSpotsSet(fullpathcorfile, key_material, emin, emax, dict_loop, None,
                         use_file=0, # if 1, reimport data from file and reset also spots properties dictionary
                         IMM=False,LUT=None,n_LUT=dict_loop['nlutmax'],angletol_list=dict_loop['list matching tol angles'],
                        nbGrainstoFind=1,
                      starting_grainindex=0,
                      MatchingRate_List=[1, 1, 1,1,1,1,1,1],
                        verbose=0, previousResults=None,
                        corfilename=corfilename)

self.pixelsize in IndexSpotsSet 0.08057
ResolutionAngstromLUT in IndexSpotsSet False

 Remaining nb of spots to index for grain #0 : 12


 **
start to index grain #0 of Material: Ge

**

providing new set of matrices Using Angles LUT template matching
nbspots 12
NBMAXPROBED 6
nbspots 12
set_central_spots_hkl None
Computing LUT from material data
Compute LUT for indexing Ge spots in LauePattern
Build angles LUT with latticeparameters
[ 5.657499999999999  5.657499999999999  5.657499999999999
 90.                90.                90.               ]
and n=3
MaxRadiusHKL False
cubicSymmetry True
Central set of exp. spotDistances from spot_index_central_list probed
self.absolute_index [ 0  1  2  3  4  5  6  7  8  9 10 11]
spot_index_central_list [0]
[0]
LUT is not None when entering getOrientMatrices()
set_central_spots_hkl None
set_central_spots_hkl_list [None]
cubicSymmetry True
LUT_tol_angle 0.5
---***------------------------------------------------*
Calculating all possible matrices from exp spot #0 and the 5 other(s)
hkl in getOrientMatrices None <class 'NoneType'>
using LUTcubic
LUTcubic is None for k_centspot_index 0 in getOrientMatrices()
hkl1 in matrices_from_onespot_hkl() [[1 0 0]
 [1 1 0]
 [1 1 1]
 [2 1 0]
 [2 1 1]
 [2 2 1]
 [3 1 0]
 [3 1 1]
 [3 2 1]
 [3 2 2]
 [3 3 1]
 [3 3 2]]
Computing hkl2 list for specific or cubic LUT in matrices_from_onespot_hkl()
Calculating LUT in PlanePairs_from2sets()
Looking up planes pairs in LUT from exp. spots (0, 1):
Looking up planes pairs in LUT from exp. spots (0, 2):
Looking up planes pairs in LUT from exp. spots (0, 3):
Looking up planes pairs in LUT from exp. spots (0, 4):
Looking up planes pairs in LUT from exp. spots (0, 5):
calculating matching rates of solutions for exp. spots [0, 1]
calculating matching rates of solutions for exp. spots [0, 2]
calculating matching rates of solutions for exp. spots [0, 3]
calculating matching rates of solutions for exp. spots [0, 4]


return best matrix and matching scores for the one central_spot

-----------------------------------------
results:
matrix:                                         matching results
[-0.211852735694566  0.092255643652867 -0.972937466948891]        res: [20.0, 162.0] 0.014 12.35
[-0.775856536468367  0.58951816141498   0.22475536073965 ]        spot indices [0 1]
[ 0.594300563948835  0.802473664571131 -0.053318452339475]        planes [[1.0, 3.0, 2.0], [1.0, 1.0, 1.0]]

Number of matrices found (nb_sol):  1
set_central_spots_hkl in FindOrientMatrices None

-----------------------------------------
results:
matrix:                                         matching results
[-0.211852735694566  0.092255643652867 -0.972937466948891]        res: [20.0, 162.0] 0.014 12.35
[-0.775856536468367  0.58951816141498   0.22475536073965 ]        spot indices [0 1]
[ 0.594300563948835  0.802473664571131 -0.053318452339475]        planes [[1.0, 3.0, 2.0], [1.0, 1.0, 1.0]]

Nb of potential orientation matrice(s) UB found: 1
[array([[-0.211852735694566,  0.092255643652867, -0.972937466948891],
       [-0.775856536468367,  0.58951816141498 ,  0.22475536073965 ],
       [ 0.594300563948835,  0.802473664571131, -0.053318452339475]])]
Nb of potential UBs  1

Working with a new stack of orientation matrices
MATCHINGRATE_THRESHOLD_IAL= 100.0
has not been reached! All potential solutions have been calculated
taking the first one only.
bestUB object <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>


---------------refining grain orientation and strain #0-----------------


 refining grain #0 step -----0

bestUB <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
matrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
For angular tolerance 0.50 deg
Nb of pairs found / nb total of expected spots: 12/176
Matching Rate : 6.82
Nb missing reflections: 164

grain #0 : 12 links to simulated spots have been found
*********mean pixel deviation    0.560750282710606     ******
Initial residues [0.053680370172309 0.013739858524874 0.921977335411896 0.403270956234836
 0.919825854310187 0.785969463406447 0.565019172757509 1.127873079813964
 0.363514793614926 0.412635402450867 0.711008521607465 0.450488584221994]
---------------------------------------------------



***********************
first error with initial values of: ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

*********mean pixel deviation    0.560750282710606     ******


***********************
Fitting parameters:   ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

With initial values [1. 1. 0. 0. 0. 0. 0. 0.]
code results 1
nb iterations 1767
mesg Both actual and predicted relative reductions in the sum of squares
  are at most 0.000000
strain_sol [ 1.001128981010799e+00  9.993806401299155e-01  8.449040381845989e-04
 -8.486913595751131e-04  3.520626401662759e-04 -2.714612741167435e-02
  3.054889720130747e-02  5.311773668297186e-02]


 **********  End of Fitting  -  Final errors  **************


*********mean pixel deviation    0.3158807195732847     ******
devstrain, lattice_parameter_direct_strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657424223234738  5.651101185787196  5.661104877237695
 90.01741959362538  89.9544419036642   90.04747664598754 ]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
devstrain1, lattice_parameter_direct_strain1 [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
final lattice_parameters [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
UB and strain refinement completed
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8c98baa20>
matrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
For angular tolerance 0.50 deg
Nb of pairs found / nb total of expected spots: 12/177
Matching Rate : 6.78
Nb missing reflections: 165

grain #0 : 12 links to simulated spots have been found
GoodRefinement condition is  True
nb_updates 12 compared to 6


 refining grain #0 step -----1

bestUB <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
matrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
For angular tolerance 0.50 deg
Nb of pairs found / nb total of expected spots: 12/176
Matching Rate : 6.82
Nb missing reflections: 164

grain #0 : 12 links to simulated spots have been found
*********mean pixel deviation    0.560750282710606     ******
Initial residues [0.053680370172309 0.013739858524874 0.921977335411896 0.403270956234836
 0.919825854310187 0.785969463406447 0.565019172757509 1.127873079813964
 0.363514793614926 0.412635402450867 0.711008521607465 0.450488584221994]
---------------------------------------------------



***********************
first error with initial values of: ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

*********mean pixel deviation    0.560750282710606     ******


***********************
Fitting parameters:   ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

With initial values [1. 1. 0. 0. 0. 0. 0. 0.]
code results 1
nb iterations 1767
mesg Both actual and predicted relative reductions in the sum of squares
  are at most 0.000000
strain_sol [ 1.001128981010799e+00  9.993806401299155e-01  8.449040381845989e-04
 -8.486913595751131e-04  3.520626401662759e-04 -2.714612741167435e-02
  3.054889720130747e-02  5.311773668297186e-02]


 **********  End of Fitting  -  Final errors  **************


*********mean pixel deviation    0.3158807195732847     ******
devstrain, lattice_parameter_direct_strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657424223234738  5.651101185787196  5.661104877237695
 90.01741959362538  89.9544419036642   90.04747664598754 ]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
devstrain1, lattice_parameter_direct_strain1 [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
final lattice_parameters [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
UB and strain refinement completed
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8c98ba9b0>
matrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
For angular tolerance 0.50 deg
Nb of pairs found / nb total of expected spots: 12/177
Matching Rate : 6.78
Nb missing reflections: 165

grain #0 : 12 links to simulated spots have been found
GoodRefinement condition is  True
nb_updates 12 compared to 6


 refining grain #0 step -----2

bestUB <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
matrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
For angular tolerance 0.20 deg
Nb of pairs found / nb total of expected spots: 12/176
Matching Rate : 6.82
Nb missing reflections: 164

grain #0 : 12 links to simulated spots have been found
*********mean pixel deviation    0.560750282710606     ******
Initial residues [0.053680370172309 0.013739858524874 0.921977335411896 0.403270956234836
 0.919825854310187 0.785969463406447 0.565019172757509 1.127873079813964
 0.363514793614926 0.412635402450867 0.711008521607465 0.450488584221994]
---------------------------------------------------



***********************
first error with initial values of: ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

*********mean pixel deviation    0.560750282710606     ******


***********************
Fitting parameters:   ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

With initial values [1. 1. 0. 0. 0. 0. 0. 0.]
code results 1
nb iterations 1767
mesg Both actual and predicted relative reductions in the sum of squares
  are at most 0.000000
strain_sol [ 1.001128981010799e+00  9.993806401299155e-01  8.449040381845989e-04
 -8.486913595751131e-04  3.520626401662759e-04 -2.714612741167435e-02
  3.054889720130747e-02  5.311773668297186e-02]


 **********  End of Fitting  -  Final errors  **************


*********mean pixel deviation    0.3158807195732847     ******
devstrain, lattice_parameter_direct_strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657424223234738  5.651101185787196  5.661104877237695
 90.01741959362538  89.9544419036642   90.04747664598754 ]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
devstrain1, lattice_parameter_direct_strain1 [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
final lattice_parameters [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
UB and strain refinement completed
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8cf573a90>
matrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
For angular tolerance 0.20 deg
Nb of pairs found / nb total of expected spots: 12/177
Matching Rate : 6.78
Nb missing reflections: 165

grain #0 : 12 links to simulated spots have been found
GoodRefinement condition is  True
nb_updates 12 compared to 6


 refining grain #0 step -----3

bestUB <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7ddc50>
matrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211852735694566  0.092255643652867 -0.972937466948891]
 [-0.775856536468367  0.58951816141498   0.22475536073965 ]
 [ 0.594300563948835  0.802473664571131 -0.053318452339475]]
For angular tolerance 0.20 deg
Nb of pairs found / nb total of expected spots: 12/176
Matching Rate : 6.82
Nb missing reflections: 164

grain #0 : 12 links to simulated spots have been found
*********mean pixel deviation    0.560750282710606     ******
Initial residues [0.053680370172309 0.013739858524874 0.921977335411896 0.403270956234836
 0.919825854310187 0.785969463406447 0.565019172757509 1.127873079813964
 0.363514793614926 0.412635402450867 0.711008521607465 0.450488584221994]
---------------------------------------------------



***********************
first error with initial values of: ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

*********mean pixel deviation    0.560750282710606     ******


***********************
Fitting parameters:   ['b/a', 'c/a', 'a12', 'a13', 'a23', 'theta1', 'theta2', 'theta3']

***********************

With initial values [1. 1. 0. 0. 0. 0. 0. 0.]
code results 1
nb iterations 1767
mesg Both actual and predicted relative reductions in the sum of squares
  are at most 0.000000
strain_sol [ 1.001128981010799e+00  9.993806401299155e-01  8.449040381845989e-04
 -8.486913595751131e-04  3.520626401662759e-04 -2.714612741167435e-02
  3.054889720130747e-02  5.311773668297186e-02]


 **********  End of Fitting  -  Final errors  **************


*********mean pixel deviation    0.3158807195732847     ******
devstrain, lattice_parameter_direct_strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657424223234738  5.651101185787196  5.661104877237695
 90.01741959362538  89.9544419036642   90.04747664598754 ]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
devstrain1, lattice_parameter_direct_strain1 [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]] [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
final lattice_parameters [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
UB and strain refinement completed
True it is an OrientMatrix object
Orientation <LaueTools.indexingSpotsSet.OrientMatrix object at 0x7fb8ec7bc128>
matrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
*nb of selected spots in AssignHKL*** 12
UBOrientMatrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
For angular tolerance 0.20 deg
Nb of pairs found / nb total of expected spots: 12/177
Matching Rate : 6.78
Nb missing reflections: 165

grain #0 : 12 links to simulated spots have been found
GoodRefinement condition is  True
nb_updates 12 compared to 6

---------------------------------------------
indexing completed for grain #0 with matching rate 6.78
---------------------------------------------

transform matrix to matrix with lowest Euler Angles
start
 [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
final
 [[ 0.97230572627369   0.211415207301911  0.091252946262469]
 [-0.224552051799525  0.77573594328912   0.590041596352251]
 [ 0.054088075690982 -0.594613709497768  0.803610914885283]]
hkl [[2. 6. 4.]
 [3. 3. 3.]
 [5. 3. 3.]
 [1. 3. 5.]
 [6. 2. 4.]
 [5. 1. 3.]
 [1. 3. 3.]
 [6. 4. 6.]
 [4. 2. 6.]
 [4. 2. 2.]
 [3. 5. 3.]
 [2. 2. 4.]]
new hkl (min euler angles) [[-4. -2.  6.]
 [-3. -3.  3.]
 [-3. -5.  3.]
 [-5. -1.  3.]
 [-4. -6.  2.]
 [-3. -5.  1.]
 [-3. -1.  3.]
 [-6. -6.  4.]
 [-6. -4.  2.]
 [-2. -4.  2.]
 [-3. -3.  5.]
 [-4. -2.  2.]]
UB before [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
new UB (min euler angles) [[ 0.97230572627369   0.211415207301911  0.091252946262469]
 [-0.224552051799525  0.77573594328912   0.590041596352251]
 [ 0.054088075690982 -0.594613709497768  0.803610914885283]]
writing fit file -------------------------
for grainindex= 0
self.dict_grain_matrix[grain_index] [[ 0.97230572627369   0.211415207301911  0.091252946262469]
 [-0.224552051799525  0.77573594328912   0.590041596352251]
 [ 0.054088075690982 -0.594613709497768  0.803610914885283]]
self.refinedUBmatrix [[-0.211415207301911  0.091252946262469 -0.97230572627369 ]
 [-0.77573594328912   0.590041596352251  0.224552051799525]
 [ 0.594613709497768  0.803610914885283 -0.054088075690982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
new UBs matrix in q= UBs G (s for strain)
strain_direct [[-1.339403716515974e-05 -4.138432477238585e-04  3.978226745502020e-04]
 [-4.138432477238585e-04 -1.131375039302607e-03 -1.517818975573709e-04]
 [ 3.978226745502020e-04 -1.517818975573709e-04  6.255721962393768e-04]]
deviatoric strain [[ 0.000159671589578 -0.000413843247724  0.00039782267455 ]
 [-0.000413843247724 -0.00095830941256  -0.000151781897557]
 [ 0.00039782267455  -0.000151781897557  0.000798637822982]]
For comparison: a,b,c are rescaled with respect to the reference value of a = 5.657500 Angstroms
lattice_parameter_direct_strain [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
final lattice_parameters [ 5.657499999999999  5.651176877860324  5.661180703302433
 90.01741959362538  89.9544419036642   90.04747664598754 ]
File : Ge0001_g0.fit written in /home/micha/LaueToolsPy3/LaueTools/notebooks
Experimental experimental spots indices which are not indexed []
Missing reflections grainindex is -100 for indexed grainindex 0
within angular tolerance 0.500

 Remaining nb of spots to index for grain #1 : 0

12 spots have been indexed over 12
indexing rate is --- : 100.0 percents
indexation of short_Ge0001.cor is completed
for the 1 grain(s) that has(ve) been indexed as requested
Leaving Index and Refine procedures...

index_grain_retrieve=0
print("number of indexed spots", len(DataSet.getallIndexedSpotsallData()[index_grain_retrieve]))

number of indexed spots 12

Results of indexation can be found in attributes or through methods

spotsdata=DataSet.getSummaryallData()
print("first 2 indexed spots properties\n")
print('#spot  #grain 2theta chi X Y I h k l Energy')
print(spotsdata[:2])

first 2 indexed spots properties

#spot  #grain 2theta chi X Y I h k l Energy
[[ 0.000000000000000e+00  0.000000000000000e+00  6.035945800000000e+01
   2.648319100000000e+01  6.261200000000000e+02  1.661280000000000e+03
   1.582539000000000e+04 -4.000000000000000e+00 -2.000000000000000e+00
   6.000000000000000e+00  1.632366988464985e+01]
 [ 1.000000000000000e+00  0.000000000000000e+00  7.821582100000001e+01
   1.638153000000000e+00  1.027110000000000e+03  1.293280000000000e+03
   7.093127000000000e+04 -3.000000000000000e+00 -3.000000000000000e+00
   3.000000000000000e+00  9.031851548397370e+00]]

print('#grain  : [Npairs = Nb pairs with tolerance angle %.4f, 100*Npairs/Ndirections theo.]'%dict_loop['list matching tol angles'][-1])
DataSet.dict_grain_matching_rate

#grain  : [Npairs = Nb pairs with tolerance angle 0.2000, 100*Npairs/Ndirections theo.]

{0: [12, 6.779661016949152]}

print("#grain  : deviatoric strain")
DataSet.dict_grain_devstrain

#grain  : deviatoric strain

{0: array([[ 0.000159671589578, -0.000413843247724,  0.00039782267455 ],
        [-0.000413843247724, -0.00095830941256 , -0.000151781897557],
        [ 0.00039782267455 , -0.000151781897557,  0.000798637822982]])}

#RefinedUB= DataSet.dict_grain_matrix
print("#grain  : refined UB matrix")
DataSet.dict_grain_matrix

#grain  : refined UB matrix

{0: array([[ 0.97230572627369 ,  0.211415207301911,  0.091252946262469],
        [-0.224552051799525,  0.77573594328912 ,  0.590041596352251],
        [ 0.054088075690982, -0.594613709497768,  0.803610914885283]])}

print([DataSet.indexed_spots_dict[k] for k in range(10)])

[[0, 60.359458, 26.483191, 626.12, 1661.28, 15825.39, array([-4., -2.,  6.]), 16.323669884649853, 0, 1], [1, 78.215821, 1.638153, 1027.11, 1293.28, 70931.27, array([-3., -3.,  3.]), 9.03185154839737, 0, 1], [2, 68.680451, -15.358122, 1288.11, 1460.16, 22795.07, array([-3., -5.,  3.]), 12.73794897550435, 0, 1], [3, 108.452917, 37.749461, 383.77, 754.58, 4400.61, array([-5., -1.,  3.]), 7.989738078276174, 0, 1], [4, 83.349535, -27.458061, 1497.4, 1224.7, 13145.99, array([-4., -6.,  2.]), 12.327936233758937, 0, 1], [5, 82.072076, -35.89243, 1672.67, 1258.62, 13318.81, array([-3., -5.,  1.]), 9.870774398536632, 0, 1], [6, 81.771257, 30.38247, 548.25, 1260.32, 6137.87, array([-3., -1.,  3.]), 7.2986772558942405, 0, 1], [7, 91.798221, -8.309941, 1176.09, 1086.19, 11799.93, array([-6., -6.,  4.]), 14.309911950813975, 0, 1], [8, 120.59561, -8.92066, 1183.27, 598.92, 17182.88, array([-6., -4.,  2.]), 9.435284238042113, 0, 1], [9, 64.329767, -20.824155, 1379.17, 1553.58, 51933.84, array([-2., -4.,  2.]), 10.087272916663885, 0, 1]]