From 5e6aad6e2e491f3845d86a4ee25db800e8b77df0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Sat, 9 Nov 2024 13:47:15 -0500 Subject: [PATCH] STYLE: Lint DWI GP estimation notebook Lint DWI GP estimation notebook. Take advantage of the commit to remove the unused random number generator. --- docs/notebooks/dwi_gp_estimation.ipynb | 36 ++++++++++++++------------ 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/docs/notebooks/dwi_gp_estimation.ipynb b/docs/notebooks/dwi_gp_estimation.ipynb index 2cce4b3e..a26dbcb4 100644 --- a/docs/notebooks/dwi_gp_estimation.ipynb +++ b/docs/notebooks/dwi_gp_estimation.ipynb @@ -29,23 +29,9 @@ "from dipy.core.gradients import get_bval_indices\n", "from dipy.io import read_bvals_bvecs\n", "from dipy.segment.mask import median_otsu\n", - "\n", "from scipy.ndimage import binary_dilation\n", "from skimage.morphology import ball\n", "\n", - "from nireports.reportlets.modality.dwi import plot_dwi" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "id": "69a3bc6b4fbe7036", - "metadata": {}, - "outputs": [], - "source": [ - "seed = 1234\n", - "rng = np.random.default_rng(seed)\n", - "\n", "name = \"sherbrooke_3shell\"\n", "\n", "dwi_fname, bval_fname, bvec_fname = dpd.get_fnames(name=name)\n", @@ -131,6 +117,8 @@ } ], "source": [ + "from nireports.reportlets.modality.dwi import plot_dwi\n", + "\n", "affine = nib.load(dwi_fname).affine\n", "plot_dwi(shell_data[..., dwi_vol_idx], affine, gradient=np.concatenate((np.squeeze(X_test), [1000])), output_file=\"sherbrooke_3shell_b1k_data.svg\")" ] @@ -221,7 +209,14 @@ "output_type": "display_data" } ], - "source": "plot_dwi(dwi_sim, affine, gradient=np.concatenate((np.squeeze(X_test), [1000])), output_file=\"sherbrooke_3shell_b1k_gp_noopt_pred.svg\")" + "source": [ + "plot_dwi(\n", + " dwi_sim,\n", + " affine,\n", + " gradient=np.concatenate((np.squeeze(X_test), [1000])),\n", + " output_file=\"sherbrooke_3shell_b1k_gp_noopt_pred.svg\",\n", + ")" + ] }, { "cell_type": "code", @@ -449,8 +444,15 @@ ], "source": [ "plot_dwi(dwi_sim, affine, gradient=np.concatenate((np.squeeze(X_test), [1000])))\n", - "plot_dwi(shell_data[..., dwi_vol_idx], affine, gradient=np.concatenate((np.squeeze(X_test), [1000])))\n", - "plot_dwi(dwi_sim2, affine, gradient=np.concatenate((np.squeeze(X_test), [1000])), output_file=\"sherbrooke_3shell_b1k_gp_opt_pred.svg\")" + "plot_dwi(\n", + " shell_data[..., dwi_vol_idx], affine, gradient=np.concatenate((np.squeeze(X_test), [1000]))\n", + ")\n", + "plot_dwi(\n", + " dwi_sim2,\n", + " affine,\n", + " gradient=np.concatenate((np.squeeze(X_test), [1000])),\n", + " output_file=\"sherbrooke_3shell_b1k_gp_opt_pred.svg\",\n", + ")" ] } ],