Add and default to regression pattern used by Costes #5
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A simple stepper and a bisection stepper class are added by this commit. The former reduces a value (the threshold) by one per update and the latter compares the update value to its last value. If it is below zero, half a step up is made, otherwise half a step down. This is repeated a maximum of 100 times or the difference between the current and the last value (threshold) is below 1.
This is required to later print the regression method that was used.
This is now the default, because it is very likely what people expect. However, the current bisection method is still available as an option. It can produce good thresholds if the images are suited for colocalization analysis. The user has to choose what is used. The selected method is also shown in the output. Costes' regression starts at the maximum threshold and moves down the regression line one by one until the Person colocalization between both channels is zero. This is what was originally described in Costes' publication. The bisection pattern, in turn, is usually faster, but might produce different results then the sequential walk. This can happen if the function of correlations of a specific threshold combination is not monotonic.
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I can't comment on the technical approach, since I'm ignorant about colocalization. But the code quality looks great—nice patches. And in general, I am a fan of doing what people expect, instead of what will surprise them. |
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I should be able to go through this again next week and then finally merge this in. |
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I looked through everything again, think all the changes are alright and will merge this. |
tomka
added a commit
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Jul 29, 2015
Add and default to regression pattern used by Costes
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great! thanks @tomka ! |
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This pull request adds support for different regression patterns. It also adds an alternative to the current bisection method: a simple regression that decrements values one by one, just as it is used in the Costes paper. Since this is what people are likely to expect, it is now the default. The faster bisection method is still available, but has to be selected by the user.
If there are no changes requested, I'll merge this in a couple of days into master. The pull request is only used for documentation and to allow discussion about this change.