fixed pca for features > samples, and fixed pca_noise_estimate

[samcoveney]

Following on from #2678 I have attempted to do several things:

1. fix genpca to work when the number of samples (voxels) is less than the number of features (images) by modifying _pca_classifier
2. fix pca_noise_estimate to be able to use the canonical algorithm

This is a new pull request to replace #2707 which became totally corrupted for reasons I don't understand, and I simply could not fix. Sorry about that. But I addressed all comments left at the time.

[samcoveney]

Hi, I opened this around 3 weeks ago, with the original corrupted pull on 4 Jan, will it be possible to assign someone to this soon please? Again, very sorry to have needed to close the original pull because I really messed something up with git and couldn't figure it out. @jhlegarreta was helping me before my error (I implemented the suggestions).

[Garyfallidis]

Thank you @samcoveney I have assigned @ShreyasFadnavis to check your PR. You should hear from him asap. Thank you!

[skoudoro]

No worries for closing the previous one!

Apologize for the long wait, I tried to ping some expert in denoising but no feedback until now.

Overall, it looks good to me. I need to test a last time to refresh my memory since since it is was long time ago.

@arokem, @ garyfallidis, any opinions?

[samcoveney]

Thanks everyone! Looking forward to comments

[RafaelNH]

Hi @samcoveney! Thanks for your work on this! Only have 4 minor comments that I would like you to addressed. After that, I am happy that your PR is merged.

[samcoveney]

I have addressed the comments / changes and squashed everything. Thanks!
edit: then re-squashed after fixing spelling mistakes, sorry

[RafaelNH]

Thanks @samcoveney ! I don't have anything to add.

[codecov]

Codecov Report

Merging #2722 (e928a82) into master (9393354) will increase coverage by 0.10%.
The diff coverage is 85.71%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2722      +/-   ##
==========================================
+ Coverage   83.83%   83.93%   +0.10%     
==========================================
  Files         131      132       +1     
  Lines       18293    18466     +173     
  Branches     2980     3015      +35     
==========================================
+ Hits        15336    15500     +164     
- Misses       2220     2222       +2     
- Partials      737      744       +7     

Impacted Files	Coverage Δ
dipy/denoise/localpca.py	88.57% <81.81%> (-0.91%)	⬇️
dipy/reconst/dti.py	95.48% <100.00%> (ø)
dipy/tracking/streamline.py	93.83% <100.00%> (ø)

... and 5 files with indirect coverage changes

[RafaelNH]

Hi @samcoveney!
Actually I have a last comment. Since you are changing already existing DIPY procedures, can you report your changes in the dipy api_change documentation? Please create a new section for DIPY 1.7.0 and add a description of your changes there. Many thanks!

[skoudoro]

Thank you @RafaelNH and @jhlegarreta for the review.

Thank you @samcoveney for this PR.

I will wait until monday/tuesday to merge this PR, just in case there are any additional comments

[skoudoro]

Thank you for this work @samcoveney and sorry for the delay, I believed it was merged before the break....