s3fs_nifti.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import nibabel as nib\n",
    "import numpy as np\n",
    "import s3fs\n",
    "from io import BytesIO\n",
    "import gzip\n",
    "\n",
    "data = np.random.randn(100, 100, 100)\n",
    "orig_img = nib.Nifti1Image(data, np.eye(4))\n",
    "\n",
    "fname = 'bucket_name/fname.nii.gz'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "def s3fs_nifti_write(img, fname):\n",
    "    fs = s3fs.S3FileSystem()\n",
    "    bio = BytesIO()\n",
    "    file_map = img.make_file_map({'image': bio, 'header': bio})\n",
    "    img.to_file_map(file_map)\n",
    "    data = gzip.compress(bio.getvalue())\n",
    "\n",
    "    with fs.open(fname, 'wb') as f:\n",
    "        f.write(data)\n",
    "\n",
    "def s3fs_nifti_read(fname):\n",
    "    fs = s3fs.S3FileSystem()\n",
    "    with fs.open(fname) as f:\n",
    "        zz = gzip.open(f)\n",
    "        rr = zz.read()\n",
    "        bb = BytesIO(rr)\n",
    "        fh = nib.FileHolder(fileobj=bb)\n",
    "        img = nib.Nifti1Image.from_file_map({'header': fh, 'image': fh})\n",
    "\n",
    "    return img"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "s3fs_nifti_write(orig_img, fname)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "new_img = s3fs_nifti_read(fname)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "np.all(new_img.get_fdata() == orig_img.get_fdata())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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