Eigen error with refinement type 4 or 5
~/crystfel/build/indexamajig -i files.lst -o test.stream -g 5HT2b-Liu-2013-predrefine.geom \
--peaks=peakfinder8 --threshold=800 --min-pix-count=1 --min-snr=3 \
-j 1 -p 5HT2B.cell --indexing=pinkindexer --pinkIndexer-refinement-type=4 \
--wavelength-estimate=1.30459e-10 \
--camera-length-estimate=0.152003
--->
WARNING: You did not specify --int-radius.
WARNING: I will use the default values, which are probably not appropriate for your patterns.
This is what I understood your unit cell to be:
orthorhombic C, unique axis ?, right handed.
a b c alpha beta gamma
61.40 122.60 168.00 A 90.00 90.00 90.00 deg
List of indexing methods:
0: pinkIndexer-nolatt-cell (pinkIndexer using cell parameters as prior information)
Indexing parameters:
Check unit cell parameters: on
Check peak alignment: on
Refine indexing solutions: on
Multi-lattice indexing ("delete and retry"): off
Retry indexing: on
peak count used for indexing: 28
computed 0%
computed 57.1429%
indexamajig: /usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:408: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
Worker 0 was killed by signal 6
Event ID was: cxidb-21-run0135/data1/LCLS_2013_Mar23_r0135_015729_c66f.h5 // 1
Task ID was: indexing:pinkindexer
peak count used for indexing: 32
computed 0%
computed 50%
0 images processed, 0 hits (-nan%), 0 indexable (-nan% of hits, -nan% overall), 0 crystals, 0.0 images/sec.
indexamajig: /usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:408: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
Worker 0 was killed by signal 6
Event ID was: cxidb-21-run0135/data1/LCLS_2013_Mar23_r0135_015637_7d13.h5 // 2
Task ID was: indexing:pinkindexer
peak count used for indexing: 20
computed 0%
computed 80%
indexamajig: /usr/include/eigen3/Eigen/src/Core/DenseCoeffsBase.h:408: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator[](Eigen::Index) [with Derived = Eigen::Array<float, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = float; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
Worker 0 was killed by signal 6
Event ID was: cxidb-21-run0135/data1/LCLS_2013_Mar23_r0135_015609_5685.h5 // 3
Task ID was: indexing:pinkindexer
peak count used for indexing: 37
computed 0%
computed 43.2432%