Skipping views during alignment in IMOD causes mismatch in tilt register for alignments

[bbarad]

During imod patch tracking alignment, it is typical to skip some views to minimize errors. If the fine alignment is done with these views skipped, the output taSolution.log file will not include that tilt. An example file is pasted in below.

When warp imports the imod alignment, these skipped views are not accounted for, so the deltlt for tilt 2 is assigned to tilt 1 (when view 1 is skipped), deltlt for tilt 3 is assigned to tilt 2, etc. This is particularly problematic because the ultimate tilt that is included (tilt 34 in this case) gets treated as if it is completely unaligned, causing larger error.

This can be mitigated by adding dummy lines accounting for skipped views. However, the better option would be for warp to trust the view index instead of automatically indexing from 1 when it reads the taSolution file.

At minimum tilt, rotation angle is  86.43
 
 view   rotation    tilt    deltilt     mag      dmag      skew    mean resid
   2      86.4     -49.3      1.68    1.0000    0.0000      0.00      2.66
   3      86.4     -46.4      1.60    1.0000    0.0000      0.00      2.50
   4      86.4     -43.5      1.51    1.0000    0.0000      0.00      2.35
   5      86.4     -40.6      1.43    1.0000    0.0000      0.00      2.15
   6      86.4     -37.6      1.40    1.0000    0.0000      0.00      1.91
   7      86.4     -34.6      1.38    1.0000    0.0000      0.00      1.70
   8      86.4     -31.6      1.35    1.0000    0.0000      0.00      1.52
   9      86.4     -28.7      1.33    1.0000    0.0000      0.00      1.36
  10      86.4     -25.7      1.30    1.0000    0.0000      0.00      1.18
  11      86.4     -22.8      1.23    1.0000    0.0000      0.00      0.97
  12      86.4     -19.8      1.15    1.0000    0.0000      0.00      0.87
  13      86.4     -16.9      1.08    1.0000    0.0000      0.00      0.74
  14      86.4     -14.0      1.01    1.0000    0.0000      0.00      0.68
  15      86.4     -11.1      0.94    1.0000    0.0000      0.00      0.61
  16      86.4      -8.3      0.75    1.0000    0.0000      0.00      0.57
  17      86.4      -5.4      0.56    1.0000    0.0000      0.00      0.59
  18      86.4      -2.6      0.37    1.0000    0.0000      0.00      0.69
  19      86.4       0.2      0.19    1.0000    0.0000      0.00      0.79
  20      86.4       3.0      0.00    1.0000    0.0000      0.00      0.91
  21      86.4       6.2      0.22    1.0000    0.0000      0.00      1.00
  22      86.4       9.4      0.44    1.0000    0.0000      0.00      1.10
  23      86.4      12.7      0.66    1.0000    0.0000      0.00      1.12
  24      86.4      15.9      0.88    1.0000    0.0000      0.00      1.17
  25      86.4      19.1      1.11    1.0000    0.0000      0.00      1.21
  26      86.4      22.3      1.33    1.0000    0.0000      0.00      1.27
  27      86.4      25.6      1.61    1.0000    0.0000      0.00      1.30
  28      86.4      28.9      1.89    1.0000    0.0000      0.00      1.36
  29      86.4      32.2      2.17    1.0000    0.0000      0.00      1.48
  30      86.4      35.5      2.45    1.0000    0.0000      0.00      1.63
  31      86.4      38.8      2.78    1.0000    0.0000      0.00      1.83
  32      86.4      42.1      3.11    1.0000    0.0000      0.00      1.98
  33      86.4      45.4      3.45    1.0000    0.0000      0.00      2.09
  34      86.4      48.8      3.78    1.0000    0.0000      0.00      2.33