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Sparse Fascicle Model #460

Merged
merged 71 commits into from Dec 18, 2014
Merged

Sparse Fascicle Model #460

merged 71 commits into from Dec 18, 2014

Commits on Dec 13, 2014

  1. NF: Starting to implement the SFM.

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  2. RF: Make sklearn an optional package.

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  3. NF: First pass at fitting the thing.

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  4. Starting to work on signal prediction.

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  5. Abstract out the design matrix construction. Predict.

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  6. BF: Make it work with different in/out situations. 

    On to test that it does something sensible (signal-wise).
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  7. TST + BF: More testing, more fixes.

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  8. TST: More tests.

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  9. Handle errors in the ODF estimation.

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  10. When signal is zero, set params to all-zeros, not nans.

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  11. TST: update the tests.

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  12. NF: Calculate the ODF from the parameters.

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  13. RF: Cache for speed.

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  14. DOC: Small fixes in documentation.

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  15. DOC: Reference

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  16. DOC: example of SFM reconstruction + tracking.

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  17. TST: Implemented tests for new interface to linear solvers. 

    Also: cleaned up some of the imports:

    import foo.bar as bar

is prefered to:

    from foo.bar import this, that, the_other
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  18. NF: Uniform sklearn-like interface to linear solvers.

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  19. TST + BF: Test and improve the NNLS dipy.core.optimize interface. 

    Specifically, in the context of sfm
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  20. RF: Testing the SKLearnLinearSolver interface. 

    This doesn't work, but I am not sure how this should be resolved.
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  21. Try using isinstance.

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  22. BF: Need to initialize these puppies.

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  23. BF: This has to come from npt namespace.

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  24. Addressing comments from review.

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  25. BF: Apparently predict should not be an abstractmethod. 

    Also: that reference contained some non-utf chars.
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  26. BF: Assign these into variables, so that doctesting doesn't freak out.

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  27. BF: This should be the mean of the non-S0 samples.

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  28. RF: Reshape once upfront and then again at the bottom. 

    To replace the acrobatics I was doing before.
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  29. DOC: Enhanced the documentation for the sfm_design_matrix function.

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  30. BF: For some (older?) versions of python, take care of cases in which… 

    … inputs

are nans (?).
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  31. RF: Reality check.

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  32. BF: Changed the kwarg to the full 'signal'. 

    This will cause hella intermittent bugs on your Travis!
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  33. TST: Need to make sure that this works for stick response function.

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  34. TST: Add another Travis-bot to test with sklearn.

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  35. TST: We don't really need two of these tests

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  36. TST: Travising

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  37. I wonder if whitespace would help.

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  38. Get me some valid yaml

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  39. TST: This is what sklearn is called here.

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  40. RF: Enable using a 'stick' function as the response function for SFM.

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  41. TST: Test using NNLS, so that it runs on Travis.

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  42. DOC: Small addition to the explanation of the kernel.

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  43. DOC: Greek letters

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  44. PEP8

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  45. DOC: Example tweaks.

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  46. PEP8, and addressing comments in example.

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  47. PEP8, etc.

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  48. PEP8: Whitespace.

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Commits on Dec 14, 2014

  1. PEP8 + pyflakes

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  2. PEP8 and pyflakes

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  3. RF: More informative variable name.

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  4. PEP8 + pyflakes

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  5. PEP8

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  6. DOC: No need for this call to 'show'

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  7. RF: Sometimes pyflakes can be rather misleading.

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  8. PEP8: No caps in function names

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  9. DOC: Include SFM example in docs.

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  10. DOC: Small typo in SNR example. 

    Thought I would shove it in here as well. Addresses dipy#350
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  11. DOC: Small typo in simulation doc 

    Addresses dipy#383
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Commits on Dec 16, 2014

  1. DOC: More work on SFM examples.

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  2. DOC: Make this example go.

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  3. DOC: Put the SFM examples in valid_examples and examples_index.

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  4. DOC: PEP8 + pyflakes

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  5. DOC: PEP8 + pyflakes.

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  6. DOC: Move streamlines to T1.

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  7. DOC: Small pyflake.

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  8. DOC: typo and whitespace.

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  9. DOC: SFM tracking

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  10. DOC: Make it run parallel.

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Commits on Dec 17, 2014

  1. DOC: Subselect streamlines

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  2. DOC: Need to provide the number of output streamlines.

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