[Rebase] Affine Registration Workflow with Supporting Quality Metrics #1735
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…rkflow. 1) Committing to this branch all the code from the affine_registration branch (PR 1581) 2) New PR should be opened for this branch.
…ile for test cases.
… dipy_align_affine.
…of mass' transformation rather than 'translation' when the progressive flag is off.
…ix the PEP8 issue.
…value of distance metric) to validate the tests by travis.
…ilarity metric in the optimize() function of the imaffine.py file. 2) Changed the parameter documentation in the run() method of the alignpy file for improved view on the command line.
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| Returns | ||
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| affine_map : instance of AffineMap | ||
| the affine resulting affine transformation | ||
| xopt : optimal parameters | ||
| the optimal parameters (translation, rotation shear etc.) |
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How many parameters are there here? In exactly what order are they returned?
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The number of parameters depends on the transformation.
eg. 2D translation -> 2 parameters, 2D Rotation -> 1 parameter, etc........
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this flat vector of parameter build the affine_map so maybe we could just add a method in the AffineMap class to get this parameter instead of returning them, but it deserves its own PR
| The object containing the affine matrix. | ||
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| """ | ||
| np.savetxt(fname, affine) |
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Why do we need a wrapper for np.savetxt? Couldn't we just use that directly?
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Even if I have the same opinion, it is always good to have an explicit function name for the end-user. Currently, they have no "explicit official" way to save an affine matrix. I do not have a strict opinion about that, I can remove it. What do you think?
Codecov Report
@@ Coverage Diff @@
## master #1735 +/- ##
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- Coverage 84.27% 84.25% -0.02%
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Files 115 115
Lines 13606 13680 +74
Branches 2144 2156 +12
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+ Hits 11466 11526 +60
- Misses 1643 1650 +7
- Partials 497 504 +7
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This looks good to me. Anyone else want to take a look? If I don't hear anything, I'll go ahead and merge this on Friday. |
The goal of this PR is to clean and rebase #1604. Look at #1604 for more information