| /dports/science/py-dipy/dipy-1.4.1/dipy/core/ |
| H A D | gradients.py | 282 bvecs = np.asarray(bvecs, float)
304 bvecs = np.where(np.isnan(bvecs), 0, bvecs)
319 grad_table.bvecs = bvecs
390 bvecs = np.asarray(bvecs)
392 if (bvecs.shape[1] > bvecs.shape[0]) and bvecs.shape[0] > 1:
393 bvecs = bvecs.T
468 bvecs = np.asarray(bvecs)
469 if (bvecs.shape[1] > bvecs.shape[0]) and bvecs.shape[0] > 1:
470 bvecs = bvecs.T
596 bvecs = np.asarray(bvecs)
[all …]
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| /dports/science/py-dipy/dipy-1.4.1/dipy/io/ |
| H A D | gradients.py | 61 bvals, bvecs = vals[0], vals[1]
64 if bvecs is None:
65 return bvals, bvecs
67 if 3 not in bvecs.shape:
69 if bvecs.ndim != 2:
70 bvecs = bvecs[None, ...]
76 if bvecs.shape[1] != 3 and bvecs.shape[1] > bvecs.shape[0]:
77 bvecs = bvecs.T
81 return bvals, bvecs
86 if bvals.shape[0] != bvecs.shape[0]:
[all …]
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| /dports/science/py-dipy/dipy-1.4.1/dipy/core/tests/ |
| H A D | test_gradients.py | 40 npt.assert_array_equal(bt.bvecs, bvecs)
44 bvecs = np.where(np.isnan(bvecs), 0, bvecs)
46 npt.assert_array_equal(bt.bvecs, bvecs)
48 npt.assert_array_equal(bt2.bvecs, bvecs)
51 npt.assert_array_equal(bt3.bvecs, bvecs)
54 npt.assert_array_equal(bt4.bvecs, bvecs)
248 npt.assert_array_equal(gt.bvecs, bvecs)
257 npt.assert_array_equal(gt.bvecs, bvecs)
319 npt.assert_array_equal(gt.bvecs, bvecs)
373 npt.assert_equal(gt.bvecs, new_gt.bvecs)
[all …]
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| /dports/science/py-dipy/dipy-1.4.1/doc/examples/ |
| H A D | reconst_dsi.py | 34 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
35 bvecs[1:] = (bvecs[1:] /
36 np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
37 gtab = gradient_table(bvals, bvecs)
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| H A D | snr_in_cc.py | 43 bvals, bvecs = read_bvals_bvecs(hardi_bval_fname, hardi_bvec_fname) variable
44 gtab = gradient_table(bvals, bvecs)
144 idx = np.sum(gtab.bvecs, axis=-1) == 0
145 gtab.bvecs[idx] = np.inf
146 axis_X = np.argmin(np.sum((gtab.bvecs-np.array([1, 0, 0]))**2, axis=-1))
147 axis_Y = np.argmin(np.sum((gtab.bvecs-np.array([0, 1, 0]))**2, axis=-1))
148 axis_Z = np.argmin(np.sum((gtab.bvecs-np.array([0, 0, 1]))**2, axis=-1))
156 gtab.bvecs[direction], "is :", SNR)
|
| H A D | reconst_gqi.py | 38 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
39 bvecs[1:] = (bvecs[1:] /
40 np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
41 gtab = gradient_table(bvals, bvecs)
|
| H A D | reconst_shore_metrics.py | 38 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
39 bvecs[1:] = (bvecs[1:] /
40 np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
41 gtab = gradient_table(bvals, bvecs)
|
| H A D | simulate_dki.py | 35 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs) variable
44 bvecs = np.concatenate((bvecs, bvecs), axis=0) variable
51 gtab = gradient_table(bvals, bvecs)
|
| H A D | gradients_spheres.py | 111 bvecs = np.vstack((vertices, vertices)) variable
118 bvecs = np.insert(bvecs, (0, bvecs.shape[0]), np.array([0, 0, 0]), axis=0) variable
143 print(bvecs)
171 gtab = gradient_table(bvals, bvecs)
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| H A D | reconst_dsi_metrics.py | 36 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
37 bvecs[1:] = (bvecs[1:] /
38 np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
39 gtab = gradient_table(bvals, bvecs)
|
| H A D | denoise_mppca.py | 55 bvals, bvecs = read_bvals_bvecs(dwi_bval_fname, dwi_bvec_fname) variable
56 gtab = gradient_table(bvals, bvecs)
65 bvecs = gtab.bvecs variable
71 gtab = gradient_table(bvals[sel_b], bvecs[sel_b])
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| H A D | reconst_mcsd.py | 66 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
67 gtab = gradient_table(bvals, bvecs)
75 bvecs = gtab.bvecs variable
85 gtab = gradient_table(bvals[sel_b], bvecs[sel_b])
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| H A D | quick_start.py | 115 bvals, bvecs = read_bvals_bvecs(fbval, fbvec) variable
124 gtab = gradient_table(bvals, bvecs)
174 print(gtab.bvecs[:10, :])
|
| /dports/science/py-dipy/dipy-1.4.1/dipy/io/tests/ |
| H A D | test_io_gradients.py | 15 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
16 gt = gradient_table(bvals, bvecs)
18 npt.assert_array_equal(bvecs, gt.bvecs)
22 npt.assert_array_equal(bvecs_none, gt.bvecs)
30 npt.assert_raises(ValueError, read_bvals_bvecs, fbvals, bvecs)
36 new_bvecs1 = bvecs[:, :2]
46 new_bvecs2 = np.ravel(bvecs)
52 new_bvecs3 = bvecs[:-1, :]
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| /dports/science/py-dipy/dipy-1.4.1/dipy/direction/tests/ |
| H A D | test_bootstrap_direction_getter.py | 27 bvecs = vertices
29 bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
31 gtab = gradient_table(bvals, bvecs)
106 bvecs = vertices
108 bvecs = np.insert(bvecs, 0, np.array([0, 0, 0]), axis=0)
110 gtab = gradient_table(bvals, bvecs)
141 gtab = gradient_table(bvals, bvecs)
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| /dports/science/py-dipy/dipy-1.4.1/dipy/reconst/ |
| H A D | dsi.py | 108 self.bvecs = gtab.bvecs
358 qtable = np.vstack((bv, bv, bv)).T * gtab.bvecs
451 bvecs = gtab.bvecs
453 bvecs = np.append(bvecs, - bvecs[1:], axis=0)
456 gtab.bvecs = bvecs.copy()
473 bvecs = gtab.bvecs
475 bvcs = bvecs[1:]
490 bvecs2 = bvecs.copy()
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| /dports/science/py-dipy/dipy-1.4.1/dipy/reconst/tests/ |
| H A D | test_csdeconv.py | 39 gtab = gradient_table(bvals, bvecs)
81 gtab = gradient_table(bvals, bvecs)
287 gtab = gradient_table(bvals, bvecs)
350 gtab = gradient_table(bvals, bvecs)
412 gtab = gradient_table(bvals, bvecs)
454 gtab = gradient_table(bvals, bvecs)
505 gtab = gradient_table(bvals, bvecs)
525 gtab = gradient_table(bvals, bvecs)
561 gtab = gradient_table(bvals, bvecs)
588 gtab = gradient_table(bvals, bvecs)
[all …]
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| H A D | test_cross_validation.py | 36 bvecs = np.concatenate(([[0, 0, 0]], psphere.vertices))
37 bvals = np.zeros(len(bvecs)) + 1000
39 gtab = gt.gradient_table(bvals, bvecs)
69 bvecs = np.concatenate(([[0, 0, 0]], psphere.vertices))
70 bvals = np.zeros(len(bvecs)) + 1000
72 gtab = gt.gradient_table(bvals, bvecs)
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| H A D | test_dti.py | 237 bvals = np.zeros(len(bvecs)) + 1000
239 gtab = grad.gradient_table(bvals, bvecs)
516 gtab = grad.gradient_table(bval, bvecs)
553 gtab = grad.gradient_table(bval, bvecs)
599 data, bvals, bvecs = get_fnames('small_25')
600 gtab = grad.gradient_table(bvals, bvecs)
616 gtab = grad.gradient_table(bval, bvecs)
688 bvals = np.zeros(len(bvecs)) + 1000
690 gtab = grad.gradient_table(bvals, bvecs)
749 bvals = np.zeros(len(bvecs)) + 1000
[all …]
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| H A D | test_sfm.py | 61 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
62 gtab = grad.gradient_table(bvals, bvecs)
75 new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
82 new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
94 new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
101 new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
113 new_gtab = grad.gradient_table(bvals[::2], bvecs[::2])
121 new_gtab = grad.gradient_table(bvals[1][None], bvecs[1][None, :])
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| /dports/science/py-nibabel/nibabel-3.2.1/nibabel/cmdline/ |
| H A D | parrec2nii.py | 204 bvals, bvecs = pr_hdr.get_bvals_bvecs()
206 if bvecs is not None:
207 bad_mask = np.logical_and(bvals != 0, (bvecs == 0).all(axis=1))
214 bvecs = bvecs[good_mask]
249 if bvals is None and bvecs is None:
251 elif bvecs is None:
264 bvecs = apply_affine(bv_reorient, bvecs)
271 for row in bvecs.T:
|
| /dports/science/py-dipy/dipy-1.4.1/dipy/data/ |
| H A D | fetcher.py | 749 bvecs = qtdmri_scheme[:, 1:4]
754 G, bvecs, big_delta, small_delta
799 bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
800 gtab = gradient_table(bvals, bvecs)
817 bvals, bvecs = read_bvals_bvecs(fbval, fbvec)
818 gtab = gradient_table(bvals, bvecs)
846 gtab = gradient_table(bvals, bvecs)
878 bvecs[1:] = (bvecs[1:] /
879 np.sqrt(np.sum(bvecs[1:] * bvecs[1:], axis=1))[:, None])
880 gtab = gradient_table(bvals, bvecs)
[all …]
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| /dports/science/py-dipy/dipy-1.4.1/dipy/sims/tests/ |
| H A D | test_voxel.py | 20 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
21 gtab = gradient_table(bvals, bvecs)
25 bvecs_2s = np.concatenate((bvecs, bvecs), axis=0)
118 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs)
119 gtab = gradient_table(bvals, bvecs)
258 bvecs = np.asarray([[1, 0, 0], [0, 1, 0], [0, 0, 1],
261 gtab_axis = gradient_table(bvals, bvecs)
319 gtab_lte = gradient_table(gtab.bvals, gtab.bvecs, btens='LTE')
320 gtab_ste = gradient_table(gtab.bvals, gtab.bvecs, btens='STE')
347 gtab_ste = gradient_table(gtab.bvals, gtab.bvecs, btens='STE')
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| H A D | test_phantom.py | 14 bvals, bvecs = read_bvals_bvecs(fbvals, fbvecs) variable
15 bvecs[np.isnan(bvecs)] = 0
17 gtab = gradient_table(bvals, bvecs)
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| /dports/science/py-dipy/dipy-1.4.1/dipy/workflows/ |
| H A D | io.py | 95 bvecs = np.loadtxt(input_path)
97 .format(bvecs.shape))
98 rows, cols = bvecs.shape
100 bvecs = bvecs.T
101 logging.info('Bvectors are \n{0}'.format(bvecs))
102 norms = np.array([np.linalg.norm(bvec) for bvec in bvecs])
|