diff --git a/notebooks/FeatureVisualization.ipynb b/notebooks/FeatureVisualization.ipynb index a80e0161..034dcd98 100644 --- 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 index b23c9cf7..6619ff78 100644 --- 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 index f0f0711f..e7bb39ab 100644 --- 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 -} +} \ No newline at end of file diff --git a/notebooks/RadiomicsExample.ipynb b/notebooks/RadiomicsExample.ipynb index dc26c16e..93f206c7 100644 --- 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 -} +} \ No newline at end of file