Add Filter.Reduce (general dimension reduction for ImageStack) #1342
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@@ Coverage Diff @@
## master #1342 +/- ##
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+ Coverage 89.21% 89.25% +0.04%
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Files 148 149 +1
Lines 5377 5416 +39
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+ Hits 4797 4834 +37
- Misses 580 582 +2
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| ---------- | ||
| dims : Axes | ||
| one or more Axes to project over | ||
| func : Union[str, Callable] |
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why not accept just Callable?
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i like it. this is the more 'pythonic' way in scientific computing -- will be easier for numpy/pandas users to reason about i think.
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@dganguli You like what? The original or my suggestion?
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In the absence of an opposition, I think func should be a Callable.
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I think it's nice to have the string option. I think a lot of users will find it annoying to need to import numpy.amax() and this component to perform a maximum intensity projection.
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I support the string option, just for ecosystem continuity -- users are used to passing function names that are resolved by getattr, as this formalism is used a lot in scipy.spatial.distance among other packages.
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@dganguli , I think @ttung suggested that we keep |
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@ttung , I think I've addressed your comments. However, the test is failing during doc generation (see error below) and I'm not sure what it is expecting because it passes |
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@ttung, I think I have addressed your comments. Would you mind taking another look? |
kevinyamauchi
changed the title
| ---------- | ||
| dims : Axes | ||
| one or more Axes to project over | ||
| func : Union[str, Callable] |
There was a problem hiding this comment.
In the absence of an opposition, I think func should be a Callable.
Summary
As discussed in #1302, this component provides the ability to perform dimension reduction operations to
ImageStackusingDataArray.reduce(). Currently, max, mean, sum, and a user-provided can be applied across specified dimensions. Closes #1302.Testing
Testing of sum, mean, and max are performed in
starfish/core/image/_filter/test/test_reduce.pyTo Do