BUG: Fix loading parameter file in notebooks.

Some recent changes broke source code in some notebooks (wrong/missing imports, missing new lines).
AIM-Harvard · Aug 16, 2017 · 1e84396 · 1e84396
1 parent 968a962
commit 1e84396
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Showing 4 changed files with 16 additions and 17 deletions.
diff --git a/notebooks/FeatureVisualization.ipynb b/notebooks/FeatureVisualization.ipynb
@@ -78,7 +78,7 @@
    "source": [
     "# Import some libraries\n",
     "import SimpleITK as sitk\n",
-    "import radiomics"
+    "from radiomics import featureextractor"
    ]
   },
   {

diff --git a/notebooks/FeatureVisualizationWithClustering.ipynb b/notebooks/FeatureVisualizationWithClustering.ipynb
@@ -80,7 +80,7 @@
    "source": [
     "# Import some libraries\n",
     "import SimpleITK as sitk\n",
-    "import radiomics"
+    "from radiomics import featureextractor"
    ]
   },
   {

diff --git a/notebooks/FilteringEffects.ipynb b/notebooks/FilteringEffects.ipynb
@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "# Radiomics package\n",
-    "import radiomics\n",
+    "from radiomics import featureextractor\n",
     "\n",
     "import six, numpy as np"
    ]
@@ -61,7 +61,7 @@
     "import SimpleITK as sitk\n",
     "\n",
     "image = sitk.ReadImage(\"example_data/brain1_image.nrrd\")\n",
-    "label = sitk.ReadImage(\"example_data/brain1_label.nrrd\")\n"
+    "label = sitk.ReadImage(\"example_data/brain1_label.nrrd\")"
    ]
   },
   {
@@ -138,8 +138,7 @@
     "# Instantiate the extractor\n",
     "params = os.path.join(os.getcwd(), '..', 'examples', 'exampleSettings', 'Params.yaml')\n",
     "\n",
-    "extractor = featureextractor.RadiomicsFeaturesExtractor(params)",
-    "\n",
+    "extractor = featureextractor.RadiomicsFeaturesExtractor(params)\n",
     "# Construct a set of SimpleITK filter objects\n",
     "filters = {\n",
     "    \"AdditiveGaussianNoise\" : sitk.AdditiveGaussianNoiseImageFilter(),\n",
@@ -214,7 +213,7 @@
     "for key, value in six.iteritems(filters):\n",
     "    print ( \"filtering with \" + key )\n",
     "    filtered_image = value.Execute(image)\n",
-    "    results[key] = extractor.execute(filtered_image, label)\n"
+    "    results[key] = extractor.execute(filtered_image, label)"
    ]
   },
   {
@@ -239,7 +238,7 @@
    "source": [
     "# Keep an index of filters and features\n",
     "filter_index = list(sorted(filters.keys()))\n",
-    "feature_names = list(sorted(filter ( lambda k: k.startswith(\"original_\"), results[filter_index[0]] )))\n"
+    "feature_names = list(sorted(filter ( lambda k: k.startswith(\"original_\"), results[filter_index[0]] )))"
    ]
   },
   {
@@ -321,7 +320,7 @@
     "print (\"\\n\")\n",
     "print (\"Bottom 10 features with _smallest_ coefficient of variation\")\n",
     "for i in range(-11,-1):\n",
-    "    print (\"Feature: {:<50} CV: {}\".format ( cv_sorted[i], cv[cv_sorted[i]]))\n"
+    "    print (\"Feature: {:<50} CV: {}\".format ( cv_sorted[i], cv[cv_sorted[i]]))"
    ]
   }
  ],
@@ -334,7 +333,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 2.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -346,4 +345,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}
diff --git a/notebooks/RadiomicsExample.ipynb b/notebooks/RadiomicsExample.ipynb
@@ -33,7 +33,7 @@
    "outputs": [],
    "source": [
     "# Radiomics package\n",
-    "import radiomics\n",
+    "from radiomics import featureextractor\n",
     "\n",
     "import six, numpy as np"
    ]
@@ -166,10 +166,11 @@
     }
    ],
    "source": [
+    "import os\n",
     "# Instantiate the extractor\n",
     "params = os.path.join(os.getcwd(), '..', 'examples', 'exampleSettings', 'Params.yaml')\n",
     "\n",
-    "extractor = featureextractor.RadiomicsFeaturesExtractor(params)",
+    "extractor = featureextractor.RadiomicsFeaturesExtractor(params)\n",
     "result_1 = extractor.execute(image_1, label_1)\n",
     "result_2 = extractor.execute(image_2, label_2)"
    ]
@@ -239,7 +240,6 @@
     }
    ],
    "source": [
-    "\n",
     "plt.figure(figsize=(20,20))\n",
     "plt.subplot(3,1,1)\n",
     "plt.plot(feature_1)\n",
@@ -255,7 +255,7 @@
     "plt.plot(feature_1 - feature_2)\n",
     "plt.yscale('log')\n",
     "plt.title ( \"Difference\")\n",
-    "plt.show()\n"
+    "plt.show()"
    ]
   }
  ],
@@ -268,7 +268,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 2.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -280,4 +280,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}