--- a +++ b/notebooks/ni_viewer.ipynb @@ -0,0 +1,106 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import nibabel as nib\n", + "import os\n", + "from nilearn.image import crop_img\n", + "from nilearn.image import new_img_like, resample_to_img\n", + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "!ls ../brats/prediction/35" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "scrolled": true + }, + "outputs": [], + "source": [ + "src_dir = '../brats/prediction/'\n", + "subject_id = '35'\n", + "vol = nib.load(os.path.join(src_dir, subject_id, 'data_volume.nii.gz'))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "%matplotlib" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "vol.orthoview()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "sys.path.append('..')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from fetal_new import augment" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "augment.distort_image()" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.6.6" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +}