Add example for BIDS dataset in tutorial notebook

sinhaharsh · Feb 5, 2024 · a17b8c1 · a17b8c1
1 parent 72d7986
commit a17b8c1
Showing 1 changed file with 96 additions and 3 deletions.
diff --git a/docs/usage.ipynb b/docs/usage.ipynb
@@ -62,11 +62,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2023-10-12T19:27:37.395592028Z",
-     "start_time": "2023-10-12T19:27:36.813565194Z"
+     "end_time": "2024-02-05T02:47:03.236451813Z",
+     "start_time": "2024-02-05T02:46:52.707102319Z"
     }
    },
    "outputs": [],
@@ -366,6 +366,99 @@
     }
    }
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## A similar example with BIDS dataset would be:"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "True\n"
+     ]
+    }
+   ],
+   "source": [
+    "import zipfile\n",
+    "MRdataset_root = Path(__name__).resolve().parents[1]\n",
+    "DATA_ARCHIVE = MRdataset_root / 'MRdataset/tests/resources/example_bids_data.zip'\n",
+    "DATA_ROOT = Path('/tmp/')\n",
+    "with zipfile.ZipFile(DATA_ARCHIVE, 'r') as zip_ref:\n",
+    "    zip_ref.extractall(DATA_ROOT)\n",
+    "print((DATA_ROOT/'example_bids_dataset').exists())\n",
+    "bids_dataset = import_dataset(data_source=DATA_ROOT/'example_bids_dataset',\n",
+    "                               ds_format='bids')"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-05T02:50:18.509122234Z",
+     "start_time": "2024-02-05T02:50:17.116480480Z"
+    }
+   },
+   "execution_count": 8
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "data": {
+      "text/plain": "6 subjects with 542 sessions in total"
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "bids_dataset"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-05T02:50:19.656918419Z",
+     "start_time": "2024-02-05T02:50:19.650049515Z"
+    }
+   },
+   "execution_count": 9
+  },
+  {
+   "cell_type": "code",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Subject: sub-02,\n",
+      "Session: ses-perceptionLetterImage01,\n",
+      "Run: run-01,\n",
+      "Sequence: func(SPP=InvalidType,SPLS=InvalidType,TR=2.0,FC=InvalidType,SHM=InvalidType,PF=InvalidType,PATM=InvalidType,SSEQ=InvalidType,SEQV=InvalidType,DT=InvalidType,SHS=InvalidType,MRAT=InvalidType,WCWE=InvalidType,PFD=InvalidType,TCN=InvalidType,AF=InvalidType,MFS=3.0,WC=InvalidType,IOP=InvalidType,SBS=InvalidType,PAT=InvalidType,FOV=InvalidType,PS=InvalidType,PHPL=InvalidType,NAV=InvalidType,IPP=InvalidType,PPFOV=InvalidType,NLGC=InvalidType,HB=InvalidType,TI=InvalidType,MTCS=InvalidType,RCAE=InvalidType,SV=InvalidType,ST=InvalidType,PP=InvalidType,RCN=InvalidType,MAF=InvalidType,SCOP=InvalidType,IF=InvalidType,BPE=InvalidType,SQNM=InvalidType,MTS=InvalidType,BA=InvalidType,VFAF=InvalidType,ETL=InvalidType,IN=InvalidType,WW=InvalidType,SIPV=InvalidType,ACQM=InvalidType,PPCSD=InvalidType,PED=InvalidType,PES=InvalidType,MSM=InvalidType,SR=InvalidType,SMD=InvalidType,CS=InvalidType,MFR=SIEMENS,MMN=VERIO,GM=InvalidType,LIPV=InvalidType,PR=InvalidType,PBW=InvalidType,PS=InvalidType,BS=InvalidType,IT=InvalidType,R=InvalidType,SL=InvalidType,C=InvalidType,PRFIP=InvalidType,FA=80.0,EN=InvalidType,SAR=InvalidType,PI=InvalidType,TE=[0.043])\n"
+     ]
+    }
+   ],
+   "source": [
+    "seq_name = 'func'\n",
+    "for subject, session, run, sequence in dicom_dataset.traverse_horizontal(seq_name):\n",
+    "    print(f\"Subject: {subject},\\nSession: {session},\\nRun: {run},\\nSequence: {sequence}\")\n",
+    "    break"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2024-02-05T02:57:56.046980815Z",
+     "start_time": "2024-02-05T02:57:55.988220218Z"
+    }
+   },
+   "execution_count": 13
+  },
   {
    "cell_type": "markdown",
    "metadata": {},