Indexation of spots data set.
Using Class spotsSet and play with spots considered for indexation and refinement
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]]