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RF: use masks in predictions and cross-validation #714

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merged 19 commits into from Oct 26, 2015

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arokem commented Sep 18, 2015

This is an improvement on the previous API, which did not allow using masks for multi-voxel predictions, making predictions for cross-validation un-necessarily slow.

@arokem arokem changed the title from RF: use masks in predictions and cross-validation to WIP: use masks in predictions and cross-validation Sep 18, 2015

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arokem commented Sep 18, 2015

Changed to WIP, while I try out a few more things.

@arokem arokem changed the title from WIP: use masks in predictions and cross-validation to RF: use masks in predictions and cross-validation Sep 18, 2015

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arokem commented Sep 18, 2015

OK - this is ready for review. Note that many of the changes are PEP8 cleanups.

If you are interested in the functional changes this is the relevant diff:

master...315c0be

@arokem arokem force-pushed the arokem:mask-predictions branch from 25b3ce1 to 9411ae6 Oct 8, 2015

@arokem arokem force-pushed the arokem:mask-predictions branch 2 times, most recently from ef29c03 to 88dc61b Oct 16, 2015

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arokem commented Oct 18, 2015

I think I've found the source of the previous test failures: the multi-voxel prediction function was allocating an empty array for the results, and this came up with a nan ever so often, in a random way. In general, empty sure is a dangerous function!

@@ -1017,7 +1024,8 @@ def linearity(self):
.. math::
Linearity = \frac{\lambda_1-\lambda_2}{\lambda_1+\lambda_2+\lambda_3}
Linearity =
\frac{\lambda_1-\lambda_2}{\lambda_1+\lambda_2+\lambda_3}

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Question. Have you checked that breaking the line here renders fine?

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Yes - the docs render just fine. I have found a few typos in the meanwhile, so adding the fixes for that.

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Garyfallidis commented Oct 19, 2015

Okay this looks good to me. Can someone have another look?

@arokem arokem force-pushed the arokem:mask-predictions branch from a8afa19 to 188e49d Oct 19, 2015

@arokem arokem force-pushed the arokem:mask-predictions branch from 35cae5a to 7dd1a3d Oct 22, 2015

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arokem commented Oct 22, 2015

This is now rebased on current master. @MrBago or @stefanv - any chance to get one of you to take a quick look?

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stefanv commented Oct 23, 2015

This looks good to me, Ariel.

Garyfallidis added a commit that referenced this pull request Oct 26, 2015

Merge pull request #714 from arokem/mask-predictions
RF: use masks in predictions and cross-validation

@Garyfallidis Garyfallidis merged commit 6078c3a into nipy:master Oct 26, 2015

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