Mercurial > repos > greg > create_streamlines

comparison create_streamlines.py @ 4:3b5e09c727f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 28 Nov 2017 14:37:35 -0500
parents 51263bfe7b2c
children 606a712b6322
comparison
equal deleted inserted replaced
3:51263bfe7b2c 4:3b5e09c727f5
59 fvtk.add(r, vol_actor) 59 fvtk.add(r, vol_actor)
60 fvtk.add(r, vol_actor2) 60 fvtk.add(r, vol_actor2)
61 fvtk.add(r, cc_streamlines_actor) 61 fvtk.add(r, cc_streamlines_actor)
62 fvtk.add(r, cc_ROI_actor) 62 fvtk.add(r, cc_ROI_actor)
63 # Save figures 63 # Save figures
64 fvtk.record(r, n_frames=1, out_path=args.output_corpuscallosum_axial, size=(800, 800)) 64 fvtk.record(r, n_frames=1, out_path="corpuscallosum_axial.png", size=(800, 800))
65 shutil.move("corpuscallosum_axial.png", args.output_corpuscallosum_axial)
65 fvtk.camera(r, [-1, 0, 0], [0, 0, 0], viewup=[0, 0, 1]) 66 fvtk.camera(r, [-1, 0, 0], [0, 0, 0], viewup=[0, 0, 1])
66 fvtk.record(r, n_frames=1, out_path=args.output_corpuscallosum_sagittal, size=(800, 800)) 67 fvtk.record(r, n_frames=1, out_path="corpuscallosum_sagittal.png", size=(800, 800))
68 shutil.move("corpuscallosum_sagittal.png", args.output_corpuscallosum_sagittal)
67 M, grouping = utils.connectivity_matrix(cc_streamlines, labels, affine=affine, return_mapping=True, mapping_as_streamlines=True) 69 M, grouping = utils.connectivity_matrix(cc_streamlines, labels, affine=affine, return_mapping=True, mapping_as_streamlines=True)
68 M[:3, :] = 0 70 M[:3, :] = 0
69 M[:, :3] = 0 71 M[:, :3] = 0
70 plt.imshow(np.log1p(M), interpolation='nearest') 72 plt.imshow(np.log1p(M), interpolation='nearest')
71 plt.savefig(args.output_connectivity) 73 plt.savefig("connectivity.png")
74 shutil.move("connectivity.png", args.output_connectivity)
72 lr_superiorfrontal_track = grouping[11, 54] 75 lr_superiorfrontal_track = grouping[11, 54]
73 shape = labels.shape 76 shape = labels.shape
74 dm = utils.density_map(lr_superiorfrontal_track, shape, affine=affine) 77 dm = utils.density_map(lr_superiorfrontal_track, shape, affine=affine)
75 # Save density map 78 # Save density map
76 dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine) 79 dm_img = nib.Nifti1Image(dm.astype("int16"), hardi_img.affine)