fixing selectfile exercise

djarecka · djarecka · commit 33a594973254 · 2017-12-10T22:48:44.000-05:00
diff --git a/notebooks/basic_data_input.ipynb b/notebooks/basic_data_input.ipynb
@@ -242,7 +242,7 @@
    },
    "source": [
     "### Exercise 1\n",
-    "Grab T1w images from both sessions - ses-test and ses-retest for sub-01."
+    "Grab T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-01``."
    ]
   },
   {
@@ -342,7 +342,7 @@
     "sf.inputs.base_directory = '/data/ds000114'\n",
     "\n",
     "# Feed {}-based placeholder strings with values\n",
-    "sf.inputs.subject_id = ['01', '02']\n",
+    "sf.inputs.subject_id = '01'\n",
     "sf.inputs.ses_name = \"test\"\n",
     "sf.inputs.task_name = 'fingerfootlips'"
    ]
@@ -378,31 +378,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "171204-05:26:20,565 workflow INFO:\n",
-      "\t Executing node selectfiles in dir: /tmp/tmphr8gtoyw/selectfiles\n",
-      "171204-05:26:20,573 workflow INFO:\n",
-      "\t Running node \"selectfiles\" (\"nipype.interfaces.io.SelectFiles\").\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "\n",
-       "anat = ['/data/ds000114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz', '/data/ds000114/sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz']"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from nipype import SelectFiles, Node\n",
     "from os.path import abspath as opap\n",
@@ -435,51 +413,28 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
+   "cell_type": "markdown",
+   "metadata": {
+    "solution2": "hidden",
+    "solution2_first": true
+   },
+   "source": [
+    "### Exercise 2\n",
+    "Use ``SelectFile`` to select again T1w images from both sessions - ``ses-test`` and ``ses-retest`` for ``sub-01``."
+   ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "171204-14:04:03,952 workflow INFO:\n",
-      "\t Executing node selectfiles in dir: /tmp/tmpwf9hluzg/selectfiles\n",
-      "171204-14:04:03,971 workflow INFO:\n",
-      "\t Running node \"selectfiles\" (\"nipype.interfaces.io.SelectFiles\").\n"
-     ]
-    },
-    {
-     "ename": "OSError",
-     "evalue": "No files were found matching anat template: /data/ds000114/sub-01/ses-[test, retest]/anat/sub-01_ses-[test, retest]_T1w.nii.gz",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mOSError\u001b[0m                                   Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-7-f17e79c01fac>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;31m#sf.inputs.ses_name =\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     16\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 17\u001b[0;31m \u001b[0msf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutputs\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, updatehash)\u001b[0m\n\u001b[1;32m    405\u001b[0m                     self.inputs.get_traitsfree())\n\u001b[1;32m    406\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 407\u001b[0;31m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    408\u001b[0m             \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    409\u001b[0m                 \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mremove\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhashfile_unfinished\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py\u001b[0m in \u001b[0;36m_run_interface\u001b[0;34m(self, execute, updatehash)\u001b[0m\n\u001b[1;32m    515\u001b[0m         \u001b[0mold_cwd\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetcwd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    516\u001b[0m         \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moutput_dir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 517\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_result\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_command\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexecute\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    518\u001b[0m         \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mold_cwd\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    519\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py\u001b[0m in \u001b[0;36m_run_command\u001b[0;34m(self, execute, copyfiles)\u001b[0m\n\u001b[1;32m    648\u001b[0m                         self._interface.__class__.__name__)\n\u001b[1;32m    649\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 650\u001b[0;31m                 \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_interface\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    651\u001b[0m             \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mmsg\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    652\u001b[0m                 \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_save_results\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresult\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcwd\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base.py\u001b[0m in \u001b[0;36mrun\u001b[0;34m(self, **inputs)\u001b[0m\n\u001b[1;32m   1087\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1088\u001b[0m             \u001b[0mruntime\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_run_interface\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1089\u001b[0;31m             \u001b[0moutputs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maggregate_outputs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mruntime\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1090\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mException\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0me\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1091\u001b[0m             \u001b[0;32mimport\u001b[0m \u001b[0mtraceback\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base.py\u001b[0m in \u001b[0;36maggregate_outputs\u001b[0;34m(self, runtime, needed_outputs)\u001b[0m\n\u001b[1;32m   1152\u001b[0m         \"\"\"\n\u001b[1;32m   1153\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1154\u001b[0;31m         \u001b[0mpredicted_outputs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_list_outputs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1155\u001b[0m         \u001b[0moutputs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_outputs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1156\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mpredicted_outputs\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;32m/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/io.py\u001b[0m in \u001b[0;36m_list_outputs\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1322\u001b[0m                     field, filled_template)\n\u001b[1;32m   1323\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minputs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_on_empty\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1324\u001b[0;31m                     \u001b[0;32mraise\u001b[0m \u001b[0mIOError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1325\u001b[0m                 \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1326\u001b[0m                     \u001b[0mwarn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
-      "\u001b[0;31mOSError\u001b[0m: No files were found matching anat template: /data/ds000114/sub-01/ses-[test, retest]/anat/sub-01_ses-[test, retest]_T1w.nii.gz"
-     ]
-    }
-   ],
-   "source": [
-    "#DJ TODO: doesnt work!!!\n",
+   "execution_count": null,
+   "metadata": {
+    "solution2": "hidden"
+   },
+   "outputs": [],
+   "source": [
     "from nipype import SelectFiles, Node\n",
     "\n",
     "# String template with {}-based strings\n",
-    "templates = {'anat': 'sub-01/ses-[test, retest]/anat/sub-01_ses-[test, retest]_T1w.nii.gz'}\n",
+    "templates = {'anat': 'sub-01/ses-*/anat/sub-01_ses-*_T1w.nii.gz'}\n",
     "             \n",
     "\n",
     "# Create SelectFiles node\n",
@@ -494,6 +449,15 @@
     "sf.run().outputs"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# write your solution here"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
