[demianw]

What was wrong

tensor_operations.compute_all_measures stored the length-weighted variance of the per-tract scalar means under per tract distance weighted std <scalar> (the square root was missing). This is what scalar_per_tract_mean_std and scalar_compute_most report.

For the tract length, the value was already a standard deviation (lengths.std(), in mm), but the column was labelled length std (mm^2). I kept the value and fixed the label, so value and unit agree.

The change

• per tract distance weighted std <scalar> = sqrt(average((m_i - mean)**2, weights=L_i)), where m_i is the length-weighted mean of the scalar along tract i and L_i its length.
• length std (mm^2) → length std (mm) (in compute_all_measures, length_mean_std and scalar_compute_most).

This changes numeric output and a column name:

• per tract distance weighted std <scalar> values change (now the square root of the old value). Example on 100 tracts of the test .trk file with a synthetic per-point scalar fa = |sin(x)|, tract_math a.trk scalar_per_tract_mean_std fa:
  • before: per tract distance weighted std fa = 0.0028079537354601916
  • after: per tract distance weighted std fa = 0.05299012866053631
• length_mean_std and scalar_compute_most: the column length std (mm^2) is now called length std (mm); its value does not change. On the full test file, tract_math IIT3mean_left_hemisphere_small.trk length_mean_std gives 44.18812674562544 before and after. Scripts that read this column by name need updating.

Testing

• New test_compute_all_measures_std: synthetic tracts of different lengths with a constant scalar per tract; checks the length std against numpy.std, and the weighted mean/std against numpy.average-based formulas; with equal tract lengths the weighted std equals numpy.std of the per-tract values. Fails on master, passes here.
• python -m pytest -q -p no:cacheprovider tract_querier: 43 passed, 1 skipped (pre-existing unconditional skip).
• Ran the two tract_math commands above on master and on this branch.

Merge order

Touches operations.py lines 43 and 96 and appends to tests/test_tract_math.py, like #143 and #144 (textual conflicts only). Independent otherwise.

Closes #102

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