Merge pull request #581 from satra/enh/tutorial_notebook

enh: updated tutorial

Author: satra

examples/nipype_tutorial.ipynb

@@ -63,9 +63,9 @@
       "# What is Nipype?\n",
       "\n",
       "<center>\n",
-      "<img src=\"https://raw.github.com/satra/intro2nipype/master/images/nipype.png\" width=\"50%\" />\n",
+      "<img src=\"https://raw.github.com/satra/intro2nipype/master/images/nipype.png\" width=\"40%\" />\n",
       "<br>\n",
-      "created by: Arno Klein (www.mindboggle.info)\n",
+      "Figure designed and created by: Arno Klein (www.mindboggle.info)\n",
       "</center>\n"
      ]
     },
@@ -146,6 +146,35 @@
       "- part of an ecosystem"
      ]
     },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "# Python ecosystem\n",
+      "<table width=\"1024px\">\n",
+      "<tr>\n",
+      "<td colspan=\"2\"><a href=\"http://ipython.org/\"><img src=\"http://ipython.org/_static/IPy_header.png\"></a></td>\n",
+      "<td colspan=\"2\"><a href=\"http://nipy.org/\"><img src=\"http://nipy.org/_static/nipy-community-banner-gy.png\"></a></td>\n",
+      "</tr>\n",
+      "<tr>\n",
+      "<td><a href=\"http://scipy.org/\"><img src=\"http://www.scipy.org/_static/images/tutorial.png\"></a></td>\n",
+      "<td><a href=\"http://numpy.org/\"><img src=\"http://www.numpy.org/_static/numpy_logo.png\"></a></td>\n",
+      "<td><a href=\"http://pymvpa.org/\"><img src=\"http://www.pymvpa.org/_static/pymvpa_logo.jpg\" width=\"256\"></a></td>\n",
+      "<td><a href=\"http://scikit-learn.org/\"><img src=\"http://scikit-learn.org/stable/_static/scikit-learn-logo-small.png\"></a></td>\n",
+      "</tr>\n",
+      "<tr>\n",
+      "<td><a href=\"http://networkx.github.io/\"><img src=\"https://raw.github.com/networkx/networkx/master/doc/source/static/art1.png\" width=\"256\"></a></td>\n",
+      "<td><a href=\"http://matplotlib.org/\"><img src=\"http://matplotlib.org/_static/logo2.png\" width=\"256\"></a></td>\n",
+      "<td><a href=\"http://code.enthought.com/projects/mayavi/\"><img src=\"http://code.enthought.com/img/mayavi-samp.png\" width=\"256\"></a></td>\n",
+      "<td><a href=\"http://neuro.debian.net/\"><img src=\"http://neuro.debian.net/_static/button_w200.png\"></a></td>\n",
+      "</tr>\n",
+      "</table>\n"
+     ]
+    },
     {
      "cell_type": "markdown",
      "metadata": {
@@ -219,24 +248,42 @@
      "source": [
       "#Software interfaces\n",
       "\n",
-      "Currently supported (5-2-2013). `Click here for latest <http://www.mit.edu/~satra/nipype-nightly/documentation.html>`_\n",
-      "\n",
-      "- [AFNI](http://afni.nimh.nih.gov/afni)\n",
-      "- [ANTS](http://www.picsl.upenn.edu/ANTS)\n",
-      "- [BRAINS](http://www.psychiatry.uiowa.edu/mhcrc/IPLpages/BRAINS.htm)\n",
-      "- [Camino](http://www.cs.ucl.ac.uk/research/medic/camino)\n",
-      "- [Camino-TrackVis](http://www.nitrc.org/projects/camino-trackvis)\n",
-      "- [ConnectomeViewerToolkit](http://www.connectomeviewer.org)\n",
-      "- [dcm2nii](http://www.cabiatl.com/mricro/mricron/dcm2nii.html)\n",
-      "- [Diffusion Toolkit](http://www.trackvis.org/dtk)\n",
-      "- [FreeSurfer](http://freesurfer.net)\n",
-      "- [FSL](http://www.fmrib.ox.ac.uk/fsl)\n",
-      "- [MRtrx](http://www.brain.org.au/software/mrtrix/index.html)\n",
-      "- [Nipy](http://nipy.org/nipy)\n",
-      "- [Nitime](http://nipy.org/nitime)\n",
-      "- [PyXNAT](http://github.com/pyxnat)\n",
-      "- [Slicer](http://www.slicer.org)\n",
-      "- [SPM](http://www.fil.ion.ucl.ac.uk/spm)\n",
+      "Currently supported (5-2-2013). [Click here for latest](http://www.mit.edu/~satra/nipype-nightly/documentation.html)\n",
+      "\n",
+      "<style>\n",
+      ".rendered_html table{border:0px}\n",
+      ".rendered_html tr{border:0px}\n",
+      ".rendered_html td{border:0px}\n",
+      "</style>\n",
+      "\n",
+      "<table>\n",
+      "<tr>\n",
+      "<td>\n",
+      "<ul>\n",
+      "<li><a href=\"http://afni.nimh.nih.gov/afni\">AFNI</a></li>\n",
+      "<li><a href=\"http://www.picsl.upenn.edu/ANTS\">ANTS</a></li>\n",
+      "<li><a href=\"http://www.psychiatry.uiowa.edu/mhcrc/IPLpages/BRAINS.htm\">BRAINS</a></li>\n",
+      "<li><a href=\"http://www.cs.ucl.ac.uk/research/medic/camino\">Camino</a></li>\n",
+      "<li><a href=\"http://www.nitrc.org/projects/camino-trackvis\">Camino-TrackVis</a></li>\n",
+      "<li><a href=\"http://www.connectomeviewer.org\">ConnectomeViewerToolkit</a></li>\n",
+      "<li><a href=\"http://www.cabiatl.com/mricro/mricron/dcm2nii.html\">dcm2nii</a></li>\n",
+      "<li><a href=\"http://www.trackvis.org/dtk\">Diffusion Toolkit</a></li>\n",
+      "</ul>\n",
+      "</td>\n",
+      "<td>\n",
+      "<ul>\n",
+      "<li><a href=\"http://freesurfer.net\">FreeSurfer</a></li>\n",
+      "<li><a href=\"http://www.fmrib.ox.ac.uk/fsl\">FSL</a></li>\n",
+      "<li><a href=\"http://www.brain.org.au/software/mrtrix/index.html\">MRtrx</a></li>\n",
+      "<li><a href=\"http://nipy.org/nipy\">Nipy</a></li>\n",
+      "<li><a href=\"http://nipy.org/nitime\">Nitime</a></li>\n",
+      "<li><a href=\"http://github.com/pyxnat\">PyXNAT</a></li>\n",
+      "<li><a href=\"http://www.slicer.org\">Slicer</a></li>\n",
+      "<li><a href=\"http://www.fil.ion.ucl.ac.uk/spm\">SPM</a></li>\n",
+      "</ul>\n",
+      "</td>\n",
+      "</tr>\n",
+      "</table>\n",
       "\n",
       "Most used/contributed policy!\n",
       "\n",
@@ -511,7 +558,11 @@
     },
     {
      "cell_type": "markdown",
-     "metadata": {},
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
      "source": [
       "### Finding interface inputs and outputs and examples"
      ]
@@ -538,7 +589,11 @@
     },
     {
      "cell_type": "markdown",
-     "metadata": {},
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
      "source": [
       "### Creating a directory for running interfaces"
      ]
@@ -593,6 +648,17 @@
      "metadata": {},
      "outputs": []
     },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "source": [
+      "## Other ways"
+     ]
+    },
     {
      "cell_type": "code",
      "collapsed": false,
@@ -1173,7 +1239,10 @@
       "\n",
       "    'base_directory/container/parameterization/destloc/filename'\n",
       "    \n",
-      "    destloc = string[[.[@]]string[[.[@]]string]] and\n",
+      "    destloc = [@]string[[.[@]]string[[.[@]]string]...] and\n",
+      "    destloc = realigned.@parameters --> 'realigned'\n",
+      "    destloc = realigned.parameters.@1 --> 'realigned/parameters'\n",
+      "    destloc = realigned.parameters.@2 --> 'realigned/parameters'\n",
       "    filename comes from the input to the connect statement."
      ]
     },
@@ -1231,7 +1300,7 @@
      "language": "python",
      "metadata": {
       "slideshow": {
-       "slide_type": "subslide"
+       "slide_type": "-"
       }
      },
      "outputs": []
@@ -1323,30 +1392,31 @@
       }
      },
      "source": [
-      "# Or to other job managers\n",
+      "### Or to other job managers\n",
       "\n",
-      "```\n",
-      "    >>> connectedworkflow.run('PBS', plugin_args={'qsub_args': '-q many'})\n",
-      "    >>> connectedworkflow.run('SGE', plugin_args={'qsub_args': '-q many'})\n",
-      "    >>> connectedworkflow.run('LSF', plugin_args={'qsub_args': '-q many'})\n",
-      "    >>> connectedworkflow.run('Condor')\n",
-      "    >>> connectedworkflow.run('IPython')\n",
-      "```\n",
+      "- connectedworkflow.run('PBS', plugin_args={'qsub_args': '-q many'})\n",
+      "- connectedworkflow.run('SGE', plugin_args={'qsub_args': '-q many'})\n",
+      "- connectedworkflow.run('LSF', plugin_args={'qsub_args': '-q many'})\n",
+      "- connectedworkflow.run('Condor')\n",
+      "- connectedworkflow.run('IPython')\n",
       "\n",
       "### or submit graphs as a whole\n",
       "\n",
-      "```\n",
-      "    >>> connectedworkflow.run('PBSGraph', plugin_args={'qsub_args': '-q many'})\n",
-      "    >>> connectedworkflow.run('SGEGraph', plugin_args={'qsub_args': '-q many'})\n",
-      "    >>> connectedworkflow.run('CondorDAGMan')\n",
-      "```\n",
       "\n",
-      "### Current Requirement: **shared filesystem**\n"
+      "- connectedworkflow.run('PBSGraph', plugin_args={'qsub_args': '-q many'})\n",
+      "- connectedworkflow.run('SGEGraph', plugin_args={'qsub_args': '-q many'})\n",
+      "- connectedworkflow.run('CondorDAGMan')\n",
+      "\n",
+      "### Current Requirement: **SHARED FILESYSTEM**"
      ]
     },
     {
      "cell_type": "markdown",
-     "metadata": {},
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
      "source": [
       "### You can also set node specific plugin arguments"
      ]
@@ -1355,9 +1425,8 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "```\n",
-      "    >>> node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}\n",
-      "```"
+      "\n",
+      "- node.plugin_args = {'qsub_args': '-l nodes=1:ppn=3', 'overwrite': True}\n"
      ]
     },
     {
@@ -1375,30 +1444,70 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
+      "from os.path import abspath as opap\n",
+      "\n",
       "from nipype.interfaces.io import XNATSource\n",
       "from nipype.pipeline.engine import Node, Workflow\n",
       "from nipype.interfaces.fsl import BET\n",
       "\n",
+      "subject_id = 'xnat_S00001'\n",
+      "\n",
       "dg = Node(XNATSource(infields=['subject_id'],\n",
       "                     outfields=['struct'],\n",
       "                     config='/Users/satra/xnat_configs/nitrc_ir_config'),\n",
       "          name='xnatsource')\n",
       "dg.inputs.query_template = ('/projects/fcon_1000/subjects/%s/experiments/xnat_E00001'\n",
       "                            '/scans/%s/resources/NIfTI/files')\n",
       "dg.inputs.query_template_args['struct'] = [['subject_id', 'anat_mprage_anonymized']]\n",
-      "dg.inputs.subject_id = 'xnat_S00001'\n",
+      "dg.inputs.subject_id = subject_id\n",
       "\n",
       "bet = Node(BET(), name='skull_stripper')\n",
       "\n",
       "wf = Workflow(name='testxnat')\n",
       "wf.base_dir = opap('xnattest')\n",
-      "wf.connect(dg, 'struct', bet, 'in_file')\n",
-      "wf.run()"
+      "wf.connect(dg, 'struct', bet, 'in_file')"
      ],
      "language": "python",
      "metadata": {},
      "outputs": []
     },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "from nipype.interfaces.io import XNATSink\n",
+      "\n",
+      "ds = Node(XNATSink(config='/Users/satra/xnat_configs/central_config'),\n",
+      "          name='xnatsink')\n",
+      "ds.inputs.project_id = 'NPTEST'\n",
+      "ds.inputs.subject_id = 'NPTEST_xnat_S00001'\n",
+      "ds.inputs.experiment_id = 'test_xnat'\n",
+      "ds.inputs.reconstruction_id = 'bet'\n",
+      "ds.inputs.share = True\n",
+      "wf.connect(bet, 'out_file', ds, 'brain')"
+     ],
+     "language": "python",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "skip"
+      }
+     },
+     "outputs": []
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "wf.run()"
+     ],
+     "language": "python",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
+     "outputs": []
+    },
     {
      "cell_type": "markdown",
      "metadata": {
@@ -1448,7 +1557,11 @@
     },
     {
      "cell_type": "markdown",
-     "metadata": {},
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
      "source": [
       "Configurations can also be set at the node level."
      ]
@@ -1537,7 +1650,11 @@
       "wf.run()"
      ],
      "language": "python",
-     "metadata": {},
+     "metadata": {
+      "slideshow": {
+       "slide_type": "subslide"
+      }
+     },
      "outputs": []
     },
     {
@@ -1578,6 +1695,34 @@
      "metadata": {},
      "outputs": []
     },
+    {
+     "cell_type": "markdown",
+     "metadata": {
+      "slideshow": {
+       "slide_type": "slide"
+      }
+     },
+     "source": [
+      "# Summary\n",
+      "\n",
+      "\n",
+      "- This tutorial covers the concepts of Nipype\n",
+      "\n",
+      "    1. Installing and testing the installation \n",
+      "    2. Working with interfaces\n",
+      "    3. Using Nipype caching\n",
+      "    4. Creating Nodes, MapNodes and Workflows\n",
+      "    5. Getting and saving data\n",
+      "    6. Using Iterables\n",
+      "    7. Function nodes\n",
+      "    8. Distributed computation\n",
+      "    9. Connecting to databases\n",
+      "    10. Execution configuration options\n",
+      "\n",
+      "- It will allow you to reuse and debug the various workflows available in Nipype, BIPS and CPAC\n",
+      "- Please contribute new interfaces and workflows!"
+     ]
+    },
     {
      "cell_type": "code",
      "collapsed": false,
@@ -1599,4 +1744,4 @@
    "metadata": {}
   }
  ]
-}
+}