Duplicated text in reports

[tsalo]

Summary

At minimum, the optimal combination step is duplicated in our report text and visual reports. We should review the logging code to ensure that report text is only logged once, as appropriate.

In the five-echo test's current report (emphasis mine):

TE-dependence analysis was performed on input data. An adaptive mask was then generated, in which each voxel's value reflects the number of echoes with 'good' data. Multi-echo data were then optimally combined using the T2* combination method (Posse et al., 1999). Multi-echo data were then optimally combined using the T2* combination method (Posse et al., 1999). Multi-echo data were then optimally combined using the T2* combination method (Posse et al., 1999). Next, components were manually classified as BOLD (TE-dependent), non-BOLD (TE-independent), or uncertain (low-variance). This workflow used numpy (Van Der Walt, Colbert, & Varoquaux, 2011), scipy (Jones et al., 2001), pandas (McKinney, 2010), scikit-learn (Pedregosa et al., 2011), nilearn, and nibabel (Brett et al., 2019). This workflow also used the Dice similarity index (Dice, 1945; Sørensen, 1948).

Additional Detail

Next Steps

1. Review logging code
2. Eliminate duplicated text by adding a report argument to the relevant functions and setting to False when called 2+ times. See fit_loglinear for an example:
   

   tedana/tedana/decay.py

   Line 158 in 45e5ad7

   def fit_loglinear(data_cat, echo_times, adaptive_mask, report=True):

[notZaki]

As a starting point for that specific case, the duplicate messages are from multiple calls to tedana.combine._combine_t2s in the following loop:

tedana/tedana/combine.py

Lines 218 to 228 in 45e5ad7

	for echo in np.unique(adaptive_mask[mask]):
	echo_idx = adaptive_mask[mask] == echo
	if combmode == 'paid':
	combined[echo_idx, :] = _combine_paid(data[echo_idx, :echo, :],
	tes[:echo])
	else:
	t2s_ = t2s[mask, ..., np.newaxis] # mask out empty voxels/samples
	combined[echo_idx, :] = _combine_t2s(
	data[echo_idx, :echo, :], tes[:, :echo], t2s_[echo_idx, ...])