example.json

{
 "metadata": {
  "name": "",
  "signature": "sha256:b52d91c59219130c59f60a3b4d38f44bf63c0bb281cf4e10c43b025291a31537"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "## T1 and T2 Usability Report - Baseline\n",
      "\n",
      "- select the earliest scanning session based on date\n",
      "- lookup all the unique scan types in the system\n",
      "- identify T1 and T1 scans\n",
      "- lookup and compare usibiity of T1 and T2 scans"
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "import os\n",
      "import sys\n",
      "import datetime\n",
      "import ConfigParser\n",
      "import xml.etree.ElementTree as ET \n",
      "\n",
      "import pyxnat"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cfg = ConfigParser.SafeConfigParser()"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "cfg.read(os.path.expanduser('~/.ncanda.cfg'))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 3,
       "text": [
        "['/Users/nolan/.ncanda.cfg']"
       ]
      }
     ],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "user = cfg.get('xnat', 'user')\n",
      "passwd = cfg.get('xnat', 'pass')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 4
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "xnat = pyxnat.Interface(server='https://ncanda.sri.com/xnat',\n",
      "                        user=user,\n",
      "                        password=passwd,\n",
      "                        cachedir='/tmp')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 5
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "proj = xnat.select.project('accepted')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "subject = proj.subject('NCANDA_S00457')\n",
      "list(subject.experiments())"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 7,
       "text": [
        "[<Experiment Object> NCANDA_E00916, <Experiment Object> NCANDA_E00949]"
       ]
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def get_baseline_mrsession(subject):\n",
      "    dt_list = []\n",
      "    base_idx = int\n",
      "    exps = subject.experiments()\n",
      "    for exp in exps:\n",
      "        # grab the experiment date\n",
      "        dt = exp.xpath('//xnat:date')[0].text\n",
      "        year, month, day = [int(d) for d in dt.split('-')]\n",
      "        dt_list.append(datetime.date(year, month, day))\n",
      "    # find the lowest date\n",
      "    if dt_list:\n",
      "        base_idx = dt_list.index(min(dt_list))\n",
      "        return exps[base_idx]\n",
      "    else:\n",
      "        print ValueError(\"Subjet: {0} is missing a scan date\".format(subject.id()))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 56
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "exp = get_baseline_mrsession(subject)\n",
      "print exp"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "<Experiment Object> NCANDA_E00916\n"
       ]
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "# get a unique set of all scan types\n",
      "unique = set()\n",
      "for e in proj.experiments():\n",
      "    [unique.add(t) for t in e.xpath('//xnat:scan/@type')]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "unique"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 11,
       "text": [
        "{'Ax DTI 60',\n",
        " 'MoCoSeries',\n",
        " 'PhoenixZIPReport',\n",
        " 'SPGR_GRAPPA Iron',\n",
        " 'Screen Save',\n",
        " 'iron scan',\n",
        " 'localizer',\n",
        " 'ncanda-calibration-v1',\n",
        " 'ncanda-dti60b1000-v1',\n",
        " 'ncanda-dti60b1000-v1_ADC',\n",
        " 'ncanda-dti60b1000-v1_ColFA',\n",
        " 'ncanda-dti60b1000-v1_FA',\n",
        " 'ncanda-dti60b1000-v1_TENSOR',\n",
        " 'ncanda-dti60b1000-v1_TRACEW',\n",
        " 'ncanda-dti6b500pepolar-v1',\n",
        " 'ncanda-dti6b500pepolar-v1_TRACEW',\n",
        " 'ncanda-fmri-antisaccade-v1',\n",
        " 'ncanda-fmri-ringrewards-v1',\n",
        " 'ncanda-fmri-ringrewards-v1/repeat of 2',\n",
        " 'ncanda-fmri-ringrewards-v2',\n",
        " 'ncanda-fmri-ringrewards-v3',\n",
        " 'ncanda-fmri-ringrewards-v4',\n",
        " 'ncanda-grefieldmap-v1',\n",
        " 'ncanda-localizer-v1',\n",
        " 'ncanda-mprage-v1',\n",
        " 'ncanda-rsfmri-v1',\n",
        " 'ncanda-t1spgr-v1',\n",
        " 'ncanda-t2fse-v1'}"
       ]
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "t1 = ['ncanda-t1spgr-v1', 'ncanda-mprage-v1']\n",
      "t2 = ['ncanda-t2fse-v1']"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 12
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def get_scan_quality(experiment, scan_type):\n",
      "    quality = dict()\n",
      "    try:\n",
      "        for scan in experiment.scans():\n",
      "            if scan.xpath('//@type')[0] in scan_type:\n",
      "                quality.update({scan: scan.xpath('//xnat:quality')[0].text})\n",
      "    except AttributeError, e:\n",
      "        print str(e)\n",
      "    # for more than scan_type return usable\n",
      "    if len(quality.keys()) > 1:\n",
      "        print quality\n",
      "        for k,v in quality.iteritems():\n",
      "            if v == 'usable':\n",
      "                return dict(k=v)\n",
      "            else:\n",
      "                quality = dict(k=v)\n",
      "    return quality"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 61
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print get_scan_quality(exp, t1)\n",
      "print get_scan_quality(exp, t2)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "{<Scan Object> 4: 'unusable'}\n",
        "{<Scan Object> 3: 'usable'}\n"
       ]
      }
     ],
     "prompt_number": 37
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def check_t1_t2_usable(experiment):\n",
      "    quality = False\n",
      "    t1 = ['ncanda-t1spgr-v1', 'ncanda-mprage-v1']\n",
      "    t2 = ['ncanda-t2fse-v1']\n",
      "    t1_quality = get_scan_quality(experiment, t1)\n",
      "    t2_quality = get_scan_quality(experiment, t2)\n",
      "    try:\n",
      "        if t1_quality.values()[0] == t2_quality.values()[0]:\n",
      "            quality = True\n",
      "    except IndexError, e:\n",
      "        print str(e)\n",
      "    return quality"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 63
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "check_t1_t2_usable(exp)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 40,
       "text": [
        "False"
       ]
      }
     ],
     "prompt_number": 40
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def check_accepted(project):\n",
      "    result = []\n",
      "    for sub in project.subjects():\n",
      "        base_exp = get_baseline_mrsession(sub)\n",
      "        try:\n",
      "            base_dt = base_exp.xpath('//xnat:date')[0].text\n",
      "        except AttributeError, e:\n",
      "            print str(e)\n",
      "        quality = check_t1_t2_usable(base_exp)\n",
      "        try:\n",
      "            result.append((sub.id(), base_exp.id(), base_dt, quality))\n",
      "        except AttributeError, e:\n",
      "            print str(e)\n",
      "    return result\n",
      "    "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 65
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "res = check_accepted(proj)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "{<Scan Object> 2: 'unusable', <Scan Object> 16: 'usable'}\n",
        "{<Scan Object> 5: 'usable', <Scan Object> 3: 'unusable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 3: 'usable-extra', <Scan Object> 11: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 4: 'usable-extra', <Scan Object> 5: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 2: 'usable-extra', <Scan Object> 16: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "Subjet: NCANDA_S00268 is missing a scan date"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "'NoneType' object has no attribute 'xpath'\n",
        "'NoneType' object has no attribute 'scans'\n",
        "'NoneType' object has no attribute 'scans'\n",
        "list index out of range\n",
        "'NoneType' object has no attribute 'id'"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 4: 'usable', <Scan Object> 3: 'unusable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 4: 'usable', <Scan Object> 3: 'unusable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 3: 'unusable', <Scan Object> 4: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 4: 'usable', <Scan Object> 11: 'unusable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 4: 'usable', <Scan Object> 44: 'usable-extra'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "list index out of range"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 2: 'usable', <Scan Object> 3: 'usable-extra'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 3: 'unusable', <Scan Object> 24: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n",
        "{<Scan Object> 3: 'unusable', <Scan Object> 12: 'usable'}"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 66
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print res[0]\n",
      "print len(res)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "('NCANDA_S00057', 'NCANDA_E00059', '2013-01-31', True)\n",
        "526\n"
       ]
      }
     ],
     "prompt_number": 87
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "with open('usable_t1_t2_baseline.csv', 'w') as fi:\n",
      "    fi.flush()\n",
      "    hdr = ','.join(['participant', 'study', 'study_date', 't1_t2_usable'])\n",
      "    fi.writelines(hdr)\n",
      "    fi.write('\\n')\n",
      "    for row in res:\n",
      "        csv = ','.join(map(str, row))\n",
      "        fi.writelines(csv)\n",
      "        fi.write('\\n')\n",
      "    fi.close()\n",
      "    "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 90
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}