flexible grid to streamline affine generation and pathlength function #1114
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…econciling streamlines and grids with different voxel orders
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| def flexi_tvis_affine(sl_vox_order, grid_affine, dim, voxel_size): | ||
| """ Computes the mapping from voxel indices to streamline points, | ||
| reconciling streamlines and grids with different voxel orders |
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What do you mean? I think the def is against the left edge, and the docstring is indented like the rest of the functions in this file?
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Also you may want to look at the new streamline API available in DIPY. This should solve many different problems with dealing with streamline datasets. |
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On Sat, Sep 10, 2016 at 9:43 PM, Eleftherios Garyfallidis <
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Thank you for the comments. I have fixed most of the formatting issues (not sure I know what you mean regarding indentation), and commented on the number of parameters question. I also noticed that there are supposed to be two lines between each function, so I corrected that, as well. I will check out the nibabel API to see if that fixes some of these issues. |
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Hey @kesshijordan : do you understand why these test failures are happening? |
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Hi, @arokem. Thanks for checking in. I think I figured it out: I found errors I recognized when I scrolled to the bottom of the Travis build outputs. I addressed them, resubmitted to Travis, and only one build failed (#1.5; I think because of the numpy version) "AttributeError: 'numpy.ufunc' object has no attribute 'at'", referring to a use of np.minimum.at(a,(i,j,k),b)... so I replaced it with a[i,j,k]=np.minimum(a[i,j,k],b) so that all of the builds work. Is there anything else I should be looking for besides the big ERRORs? |
Current coverage is 80.96% (diff: 99.24%)@@ master #1114 diff @@
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@MrBago just pointed out that substituting a[i,j,k]=np.minimum(a[i,j,k],b) for np.minimum.at(a,(i,j,k),b) introduces errors and recommended fixing it with a little function that replaces np.minimum.at if the numpy version is less than 8. |
BF - fix _min_at function
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| sl_vox_order : string of length 3 | ||
| a string that describes the voxel order of the streamlines (ex: LPS) | ||
| grid_affine : array (4, 4), | ||
| An affine matrix describing the current space of the grid in relation to RAS+ scanner space |
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Line's too long, I believe.
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| sl_ornt = orientation_from_string(str(sl_vox_order)) | ||
| grid_ornt = nib.io_orientation(grid_affine) | ||
| reorder_grid = reorder_voxels_affine(grid_ornt, sl_ornt, np.array(dim)-1, np.array([1,1,1])) |
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Here as well: line is longer than 80 characters (PEP8)
| ---------- | ||
| tvis_hdr : header from a trackvis file | ||
| nii_aff : array (4, 4), | ||
| An affine matrix describing the current space of the grid in relation to RAS+ scanner space |
| nii_aff : array (4, 4), | ||
| An affine matrix describing the current space of the grid in relation to RAS+ scanner space | ||
| nii_data : nd array | ||
| 3D array, each with shape (x, y, z) corresponding to the shape of the brain volume, |
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Period instead of comma at the end of the sentence?
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| origin = np.dot(affine, [0, 0, 0, 1]) | ||
| assert_array_almost_equal(origin[:3], np.multiply(dim,voxel_size)-voxel_size/2) | ||
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One more linebreak here (PEP8)
| trk_point = np.dot(affine, np.append(vox_point, 1)) | ||
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| assert_array_almost_equal(trk_point[:3], (vox_point[[1, 2, 0]] + 0.5) * vsz) | ||
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One more linebreak here (PEP8)
Conflicts: dipy/tracking/tests/test_utils.py
Conflicts: dipy/tracking/tests/test_utils.py
Conflicts: dipy/tracking/tests/test_utils.py
Conflicts: dipy/tracking/tests/test_utils.py
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Thanks! Please do consider adding documentation examples using these functions, so that we can see how exactly this is useful to you. If you need a hand with that, just let me know. |
Included are two related additions :
NF: The path_length function computes the shortest path, along any streamline, between the roi and each voxel. @MrBago and I are using this for a particular project we're working on, but it could be useful in other applications.
NF: The other supporting functions (flexi tvis affine, etc.) are used in path_length, but also address a problem that I've found particularly difficult as a going-up-the-learning-curve user: mapping between grid and streamline spaces with different voxel orders. After the change to using affines instead of providing voxel sizes to functions like target, one has to sort through a lot of information in the headers to get everything in the same space. These flexi tvis affine functions are extremely helpful for painless targeting and fvtk renderings.