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Affine registration PR 3/3 #654

Merged
merged 47 commits into from Jul 26, 2015
Merged

Affine registration PR 3/3 #654

merged 47 commits into from Jul 26, 2015

Commits on Jul 16, 2015

  1. Add imaffine module and tests

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  2. RF: move both scale space classes to their own module

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  3. Add tutorial for affine registration

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    omarocegueda committed Jul 16, 2015
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  4. Display images in the affine registration tutorial

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    omarocegueda committed Jul 16, 2015
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  5. Remove non-ascii character

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    omarocegueda committed Jul 16, 2015
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  6. Restore valid examples list, fix call to overlay_slices

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  7. DOC: display sagital, coronal and axial slices in the tutorial

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  8. PEP8 : full review using Spyder. RF: use X_grid2world, X_world2grid n… 

    …aming convention
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  9. TEST: fix tests for scale space

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    omarocegueda committed Jul 16, 2015
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  10. RF: Change default optimization method to L-BFGS-B

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  11. TEST: increate test coverage, pass maxfun argument instead of maxiter… 

    … to L-BFGS-B
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  12. TEST: increase test coverage

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  13. BF: use joint PDF dimensions instead of joint gradient's. Eliminate s… 

    …pacing argument from setup (extract from matrices)
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  14. DOC: corrections and extensions to docstrings. RF: remove opt_tol arg… 

    …ument from AffineRegistration.
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  15. DOC: indicate and explain optional arguments and their defaults in im… 

    …affine module
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  16. BF: pass separate value and gradient functions for scipy<=0.12

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  17. RF: use X_grid2world and X_world2grid naming convention. BF: remove t… 

    …olerance parameter in tutorial
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  18. BF: update function signature in doctest. Add keyword to argument.

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  19. DOC: add space after 'shape' in argument descriptions

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  20. DOC: add space before colon in parameter documentation

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  21. RF: use relative imports

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  22. RF: specify sampling proportion as a float in (0,1] instead of an int… 

    …eger in (0, 100]
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  23. RF: define only one update function instead of two separate updates f… 

    …or dense and sparse.
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  24. BF: remove call to _update_dense, use unified _update instead

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  25. BF: pass parameters in call to _update. DOC: require sequence, not ne… 

    …cessarily list for level_iters.
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  26. BF: update tutorial. RF: change string option from 'origins' to 'voxe… 

    …l-origin'. RF: rename 'x0' to param0. DOC: correct/enhance docstrings.
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  27. RF: make printed messages optional by using vervosity levels.

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  28. TEST: update starting_affine argument to 'voxel-origin' instead of 'o… 

    …rigins'
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  29. PEP8: max. 79 characters per line

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  30. RF: rename value_and_gradient to distance_and_gradient. Update the tu… 

    …torial, show input images before alignment and use transform instead of warp
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  31. NF: add AffineMap class and use it instead of transform_image (removed)

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  32. RF: extend vector_fields and mattes modules to support both float32 a… 

    …nd float64 buffers. Use float64 always in imaffine.
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  33. RF: rename mattes module and its classes. Move the computation of MI … 

    …to a separate specialized class.
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  34. BF: remove reference to old mattes module

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  35. RF: return ValueError instead of returning flag for non-invertible tr… 

    …ansform. BF: remove reference to old mattes module.
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  36. RF: define gradient functions as def instead of cdef to make template… 

    … specialization cleaner.
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  37. RF: raise custom exception on singular affine. DOC: explain how affin… 

    …e operates in world coordinates.
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  38. RF: select transform method using a dictionary

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  39. RF: rename 'warp_affine' methods to 'transform_affine'

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  40. BF: cast image to float64 for linear interpolation

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Commits on Jul 23, 2015

  1. RF: remove ParzenMutualInformation (and its tests) infavor of a simpl… 

    …er MutualInformationMetric that 'has a' ParzenHistogram
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    omarocegueda committed Jul 23, 2015
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  2. RF: remove unused random sampling functions in favor of deterministic… 

    … sampling
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    omarocegueda committed Jul 23, 2015
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  3. BF: evaluate image gradient and transform Jacobian at the right point… 

    …s. TEST: make gradient tests stronger to catch this kind of errors.
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    omarocegueda committed Jul 23, 2015
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  4. TEST: check all exceptions from parzenhist module

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    omarocegueda committed Jul 23, 2015
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Commits on Jul 24, 2015

  1. BF: use right affine for inverse transform. TEST: test inverse transform

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    omarocegueda committed Jul 24, 2015
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  2. BF: update tutorial. Get max_iter from scales in the right order.

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    omarocegueda committed Jul 24, 2015
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  3. DOC: add missing blank lines in tutorial

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    omarocegueda committed Jul 24, 2015
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