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fitallb's Issues

Error when writing covariance

I receive the following traceback message when running fitallb.py on one of the included test input files (inf10.inp):

Traceback (most recent call last):
  File "fitallb.py", line 16, in <module>
    gofitallb.run(options)
  File "gofitallb.py", line 121, in run
    fit.refine(far,options.killfile)
  File "fit.py", line 581, in refine
    lsqr.refine()
  File "fit.py", line 138, in refine
    write_output.write_cor(self,i)
  File "write_output.py", line 113, in write_cor
    string = string + '%8f  ' %(lsqr.mg.covariance[('%s' %entry1, '%s' %entry2)]/(n.sqrt(lsqr.mg.covariance[('%s' %entry1, '%s' %entry1)])*n.sqrt(lsqr.mg.covariance[('%s' %entry2, '%s' %entry2)]))) 
TypeError: 'NoneType' object has no attribute '__getitem__'

Error when reading gff generated by ubi_to_gff.py

I am trying to pass the output from ImageD11/grid_index_parallel.py into FitAllB for parameter/strain analysis.

I am converting the .map file output by grid_index_parallel into a gff using ubi_to_gff.py from xfab.
I am using that .gff as "res_file" in the FitAllB input file.
I am using the .flt file output by grid_index_parallel as "flt_file" in the FitAllB input file.

I am receiving the following error message:

python2.7/site-packages/FitAllB/check_input.py:1003: RuntimeWarning: divide by zero encountered in double_scalars
  errorscale = ia*(1+lenrod*lenrod)/(lenrod*(1-0.25*ia*ia*lenrod*lenrod))
python2.7/site-packages/FitAllB/check_input.py:1006: RuntimeWarning: invalid value encountered in double_scalars
  self.errors['rodx%s' %i] = errorscale*abs(self.rod[i][0])
python2.7/site-packages/FitAllB/check_input.py:1007: RuntimeWarning: invalid value encountered in double_scalars
  self.errors['rody%s' %i] = errorscale*abs(self.rod[i][1])
python2.7/site-packages/FitAllB/check_input.py:1008: RuntimeWarning: invalid value encountered in double_scalars
  self.errors['rodz%s' %i] = errorscale*abs(self.rod[i][2])
python2.7/site-packages/FitAllB/check_input.py:1009: RuntimeWarning: invalid value encountered in double_scalars
  self.fitarg['error_rodx%s' %i] = errorscale*abs(self.rod[i][0])
python2.7/site-packages/FitAllB/check_input.py:1010: RuntimeWarning: invalid value encountered in double_scalars
  self.fitarg['error_rody%s' %i] = errorscale*abs(self.rod[i][1])
python2.7/site-packages/FitAllB/check_input.py:1011: RuntimeWarning: invalid value encountered in double_scalars
  self.fitarg['error_rodz%s' %i] = errorscale*abs(self.rod[i][2])

Here's the relevant lines in FitAllB input:

### Input files
res_file allgridout.gff
flt_file gridout.flt

Here's the first few lines of the .gff for reference:

# grainno x y z rodx rody rodz U11 U12 U13 U21 U22 U23 U31 U32 U33 eps11 eps22 eps33 eps23 eps13 eps12
0 0.205346 -0.356577 0.060300 -0.344950 0.029712 -0.307969 0.842387172708 -0.523936924444 0.125991866649 0.490187561651 0.647926107994 -0.583016220171 0.223830305501 0.552885031253 0.802632005689 -1.7661e-03 -2.1563e-03 -1.9928e-03 -3.5854e-04 -1.0047e-04 8.1756e-05
1 0.209369 -0.428516 -0.031900 0.362068 0.171121 -0.157990 0.908476388982 -0.162034783735 -0.385247166793 0.371113822548 0.736692641918 0.565295039831 0.192211293571 -0.656527745189 0.729401219097 -2.5416e-03 -1.6187e-03 -1.8283e-03 2.3781e-05 -1.0624e-04 1.9635e-04
2 0.067452 -0.408914 -0.043239 -0.376098 -0.188936 -0.197238 0.877308025079 -0.207523281253 0.432740935053 0.441259163528 0.703379777945 -0.557267654346 -0.188735210640 0.679846288300 0.708652273368 -1.2378e-03 -1.6229e-03 -1.5924e-03 -3.8125e-04 -6.4030e-04 8.8231e-05
5 0.356833 -0.454787 0.030959 -0.342677 -0.297605 -0.078189 0.843773268136 0.039259758905 0.535261938969 0.297284826039 0.796155480845 -0.527027686681 -0.446842706314 0.603817126000 0.660103381421 -1.6547e-03 -1.6810e-03 -1.7334e-03 1.7942e-04 5.0031e-04 -5.4629e-04

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