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1 #!/usr/bin/env python
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2 import argparse
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3 import numpy as np
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4 import os.path as op
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5 import nibabel as nib
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6 import dipy.core.optimize as opt
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7 import dipy.tracking.life as life
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8 import matplotlib.pyplot as plt
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9 import matplotlib
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10
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11 from dipy.viz.colormap import line_colors
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12 from dipy.viz import fvtk
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13 from mpl_toolkits.axes_grid1 import AxesGrid
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14
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15 parser = argparse.ArgumentParser()
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16 parser.add_argument('--candidates', dest='candidates', help='Candidates selection')
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17 parser.add_argument('--output_life_candidates', dest='output_life_candidates', help='Output life candidates')
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18 parser.add_argument('--output_life_optimized', dest='output_life_optimized', help='Output life optimized streamlines')
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19 parser.add_argument('--output_beta_histogram', dest='output_beta_histogram', help='Output beta histogram')
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20 parser.add_argument('--output_error_histograms', dest='output_error_histograms', help='Output error histograms')
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21 parser.add_argument('--output_spatial_errors', dest='output_spatial_errors', help='Output spatial errors')
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22
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23 args = parser.parse_args()
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24
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25 if not op.exists(args.candidates):
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26 from streamline_tools import *
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27 else:
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28 # We'll need to know where the corpus callosum is from these variables:
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29 from dipy.data import (read_stanford_labels, fetch_stanford_t1, read_stanford_t1)
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30 hardi_img, gtab, labels_img = read_stanford_labels()
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31 labels = labels_img.get_data()
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32 cc_slice = labels == 2
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33 fetch_stanford_t1()
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34 t1 = read_stanford_t1()
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35 t1_data = t1.get_data()
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36 data = hardi_img.get_data()
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37
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38 # Read the candidates from file in voxel space:
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39 candidate_sl = [s[0] for s in nib.trackvis.read(args.candidates, points_space='voxel')[0]]
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40 # Visualize the initial candidate group of streamlines
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41 # in 3D, relative to the anatomical structure of this brain.
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42 candidate_streamlines_actor = fvtk.streamtube(candidate_sl, line_colors(candidate_sl))
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43 cc_ROI_actor = fvtk.contour(cc_slice, levels=[1], colors=[(1., 1., 0.)], opacities=[1.])
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44 vol_actor = fvtk.slicer(t1_data)
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45 vol_actor.display(40, None, None)
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46 vol_actor2 = vol_actor.copy()
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47 vol_actor2.display(None, None, 35)
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48 # Add display objects to canvas.
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49 ren = fvtk.ren()
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50 fvtk.add(ren, candidate_streamlines_actor)
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51 fvtk.add(ren, cc_ROI_actor)
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52 fvtk.add(ren, vol_actor)
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53 fvtk.add(ren, vol_actor2)
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54 fvtk.record(ren, n_frames=1, out_path=args.output_life_candidates, size=(800, 800))
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55 # Initialize a LiFE model.
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56 fiber_model = life.FiberModel(gtab)
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57 # Fit the model, producing a FiberFit class instance,
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58 # that stores the data, as well as the results of the
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59 # fitting procedure.
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60 fiber_fit = fiber_model.fit(data, candidate_sl, affine=np.eye(4))
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61 fig, ax = plt.subplots(1)
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62 ax.hist(fiber_fit.beta, bins=100, histtype='step')
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63 ax.set_xlabel('Fiber weights')
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64 ax.set_ylabel('# fibers')
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65 fig.savefig(args.output_beta_histogram)
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66 # Filter out these redundant streamlines and
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67 # generate an optimized group of streamlines.
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68 optimized_sl = list(np.array(candidate_sl)[np.where(fiber_fit.beta>0)[0]])
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69 ren = fvtk.ren()
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70 fvtk.add(ren, fvtk.streamtube(optimized_sl, line_colors(optimized_sl)))
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71 fvtk.add(ren, cc_ROI_actor)
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72 fvtk.add(ren, vol_actor)
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73 fvtk.record(ren, n_frames=1, out_path=args.output_life_optimized, size=(800, 800))
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74 model_predict = fiber_fit.predict()
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75 # Focus on the error in prediction of the diffusion-weighted
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76 # data, and calculate the root of the mean squared error.
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77 model_error = model_predict - fiber_fit.data
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78 model_rmse = np.sqrt(np.mean(model_error[:, 10:] ** 2, -1))
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79 # Calculate another error term by assuming that the weight for each streamline
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80 # is equal to zero. This produces the naive prediction of the mean of the
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81 # signal in each voxel.
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82 beta_baseline = np.zeros(fiber_fit.beta.shape[0])
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83 pred_weighted = np.reshape(opt.spdot(fiber_fit.life_matrix, beta_baseline), (fiber_fit.vox_coords.shape[0], np.sum(~gtab.b0s_mask)))
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84 mean_pred = np.empty((fiber_fit.vox_coords.shape[0], gtab.bvals.shape[0]))
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85 S0 = fiber_fit.b0_signal
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86 # Since the fitting is done in the demeaned S/S0 domain,
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87 # add back the mean and then multiply by S0 in every voxel:
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88 mean_pred[..., gtab.b0s_mask] = S0[:, None]
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89 mean_pred[..., ~gtab.b0s_mask] = (pred_weighted + fiber_fit.mean_signal[:, None]) * S0[:, None]
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90 mean_error = mean_pred - fiber_fit.data
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91 mean_rmse = np.sqrt(np.mean(mean_error ** 2, -1))
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92 # Compare the overall distribution of errors
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93 # between these two alternative models of the ROI.
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94 fig, ax = plt.subplots(1)
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95 ax.hist(mean_rmse - model_rmse, bins=100, histtype='step')
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96 ax.text(0.2, 0.9,'Median RMSE, mean model: %.2f' % np.median(mean_rmse), horizontalalignment='left', verticalalignment='center', transform=ax.transAxes)
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97 ax.text(0.2, 0.8,'Median RMSE, LiFE: %.2f' % np.median(model_rmse), horizontalalignment='left', verticalalignment='center', transform=ax.transAxes)
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98 ax.set_xlabel('RMS Error')
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99 ax.set_ylabel('# voxels')
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100 fig.savefig(args.output_error_histograms)
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101 # Show the spatial distribution of the two error terms,
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102 # and of the improvement with the model fit:
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103 vol_model = np.ones(data.shape[:3]) * np.nan
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104 vol_model[fiber_fit.vox_coords[:, 0], fiber_fit.vox_coords[:, 1], fiber_fit.vox_coords[:, 2]] = model_rmse
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105 vol_mean = np.ones(data.shape[:3]) * np.nan
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106 vol_mean[fiber_fit.vox_coords[:, 0], fiber_fit.vox_coords[:, 1], fiber_fit.vox_coords[:, 2]] = mean_rmse
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107 vol_improve = np.ones(data.shape[:3]) * np.nan
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108 vol_improve[fiber_fit.vox_coords[:, 0], fiber_fit.vox_coords[:, 1], fiber_fit.vox_coords[:, 2]] = mean_rmse - model_rmse
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109 sl_idx = 49
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110 fig = plt.figure()
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111 fig.subplots_adjust(left=0.05, right=0.95)
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112 ax = AxesGrid(fig, 111, nrows_ncols = (1, 3), label_mode = "1", share_all = True, cbar_location="top", cbar_mode="each", cbar_size="10%", cbar_pad="5%")
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113 ax[0].matshow(np.rot90(t1_data[sl_idx, :, :]), cmap=matplotlib.cm.bone)
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114 im = ax[0].matshow(np.rot90(vol_model[sl_idx, :, :]), cmap=matplotlib.cm.hot)
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115 ax.cbar_axes[0].colorbar(im)
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116 ax[1].matshow(np.rot90(t1_data[sl_idx, :, :]), cmap=matplotlib.cm.bone)
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117 im = ax[1].matshow(np.rot90(vol_mean[sl_idx, :, :]), cmap=matplotlib.cm.hot)
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118 ax.cbar_axes[1].colorbar(im)
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119 ax[2].matshow(np.rot90(t1_data[sl_idx, :, :]), cmap=matplotlib.cm.bone)
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120 im = ax[2].matshow(np.rot90(vol_improve[sl_idx, :, :]), cmap=matplotlib.cm.RdBu)
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121 ax.cbar_axes[2].colorbar(im)
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122 for lax in ax:
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123 lax.set_xticks([])
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124 lax.set_yticks([])
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125 fig.savefig(args.output_spatial_errors)
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