ENH: Restructure Folders

Restructure folders to better catalog the scripts and jupyter notebooks not part of the pyradiomics core code. Example scripts, notebooks and example parameter files are now stored in the directory tree under `examples`. The `bin` folder now only contains some scripts useful for developers and for specific use cases. These include a script to generate and add a baseline for a new featureclass and a script to resample a mask to the image geometry. Update the references to these files where necessary in the documentation.
jcd-gh · May 9, 2017 · b668158 · b668158
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -42,8 +42,8 @@ jobs:
           name: Install test data
           command: |
             cp -r data /tmp/example_data
-            cp bin/Params.yaml /tmp
-            cp -r bin/Notebooks/*.ipynb /tmp
+            cp examples/exampleSettings/Params.yaml /tmp
+            cp -r examples/Notebooks/*.ipynb /tmp
             # helloFeatureClass is not ready for inclusion yet, so isn't being tested
             rm -f /tmp/hello*.ipynb
       - run:

diff --git a/docs/faq.rst b/docs/faq.rst
@@ -58,9 +58,10 @@ For various reasons, both image and mask must have the same geometry (i.e. same
 when passed the feature classes. To this end PyRadiomics includes checks in the pipeline to ensure this is the case.
 If resampling is enabled, the mask is allowed to be of a different geometry, so long as the bounding box of the Region
 of Interest (ROI) represents a physical space that is within the image. If resampling is disabled, mask and image are
-required to be of the same geometry. For more information on resampling, see :py:func:`~imageoperations.resampleImage`.
-For more information on the mask checks, see :py:func:`~imageoperations.checkMask`. Alternatively, you could also
-resample the mask to image space. An example of this is provided in ``bin\resampleMask.py``.
+required to be of the same geometry. For more information on resampling, see
+:py:func:`~radiomics.imageoperations.resampleImage`. For more information on the mask checks, see
+:py:func:`~radiomics.imageoperations.checkMask`. Alternatively, you could also resample the mask to image space. An
+example of this is provided in ``bin/resampleMask.py``.
 
 **What modalities does PyRadiomics support?**
 

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -46,15 +46,15 @@ Example
 
 * The sample sample data is provided in ``pyradiomics/data``
 
-* Use `jupyter <http://jupyter.org/>`_ to run the helloRadiomics example, located in ``pyradiomics/bin/Notebooks``
+* Use `jupyter <http://jupyter.org/>`_ to run the helloRadiomics example, located in ``pyradiomics/examples/Notebooks``
 
 * Jupyter can also be used to run the example notebook as shown in the instruction video
 
-  * The example notebook can be found in ``pyradiomics/bin/Notebooks``
+  * The example notebook can be found in ``pyradiomics/examples/Notebooks``
 
-  * The parameter file used in the instruction video is available in ``pyradiomics/bin``
+  * The parameter file used in the instruction video is available in ``pyradiomics/examples/exampleSettings``
 
-* If jupyter is not installed, run the python script alternative (``pyradiomics/bin/helloRadiomics.py``):
+* If jupyter is not installed, run the python script alternative (``pyradiomics/examples/helloRadiomics.py``):
 
   * ``python helloRadiomics.py``
 
@@ -105,7 +105,7 @@ Interactive Use
 
 * Import the necessary classes::
 
-     from radiomics import featureextractor
+     from radiomics import featureextractor, getTestCase
      import six
      import sys, os
 
@@ -117,12 +117,11 @@ Interactive Use
 
 * Store the path of your image and mask in two variables::
 
-    imageName = os.path.join(dataDir, "data", 'brain1_image.nrrd')
-    maskName = os.path.join(dataDir, "data",  'brain1_label.nrrd')
+    imageName, maskName = getTestCase('brain1', dataDir)
 
 * Also store the path to the file containing the extraction settings::
 
-    params = os.path.join(dataDir, "bin", "Params.yaml")
+    params = os.path.join(dataDir, "examples", "exampleSettings", "Params.yaml")
 
 * Instantiate the feature extractor class with the parameter file::
 
@@ -160,7 +159,7 @@ Using feature classes directly
 
 * Import the necessary classes::
 
-     from radiomics import firstorder, glcm, imageoperations, shape, glrlm, glszm
+     from radiomics import firstorder, glcm, imageoperations, shape, glrlm, glszm, getTestCase
      import SimpleITK as sitk
      import six
      import sys, os
@@ -173,8 +172,7 @@ Using feature classes directly
 
 * Use SimpleITK to read a the brain image and mask::
 
-     imageName = str(dataDir + os.path.sep + 'brain1_image.nrrd')
-     maskName = str(dataDir + os.path.sep + 'brain1_label.nrrd')
+     imageName, maskName = getTestCase('brain1', dataDir)
      image = sitk.ReadImage(imageName)
      mask = sitk.ReadImage(maskName)
 

diff --git a/bin/Notebooks/FeatureVisualization.ipynb → ...ples/Notebooks/FeatureVisualization.ipynb b/bin/Notebooks/FeatureVisualization.ipynb → ...ples/Notebooks/FeatureVisualization.ipynb
diff --git a/.../FeatureVisualizationWithClustering.ipynb → .../FeatureVisualizationWithClustering.ipynb b/.../FeatureVisualizationWithClustering.ipynb → .../FeatureVisualizationWithClustering.ipynb
diff --git a/bin/Notebooks/FilteringEffects.ipynb → examples/Notebooks/FilteringEffects.ipynb b/bin/Notebooks/FilteringEffects.ipynb → examples/Notebooks/FilteringEffects.ipynb
diff --git a/bin/Notebooks/PyRadiomics Example.ipynb → examples/Notebooks/PyRadiomics Example.ipynb b/bin/Notebooks/PyRadiomics Example.ipynb → examples/Notebooks/PyRadiomics Example.ipynb
@@ -58,9 +58,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "repositoryRoot, relative path: E:\\Git-Repos\\pyradiomics\\bin\\Notebooks\\..\\..\n",
+      "repositoryRoot, relative path: E:\\Git-Repos\\pyradiomics\\examples\\Notebooks\\..\\..\n",
       "repositoryRoot, absolute path: E:\\Git-Repos\\pyradiomics\n",
-      "Parameter file, absolute path: E:\\Git-Repos\\pyradiomics\\bin\\Params.yaml\n"
+      "Parameter file, absolute path: E:\\Git-Repos\\pyradiomics\\examples\\exampleSettings\\Params.yaml\n"
      ]
     }
    ],
@@ -73,11 +73,11 @@
     "# Get the testCase\n",
     "imagePath, maskPath = radiomics.getTestCase('brain1', repositoryRoot)\n",
     "\n",
-    "if imageName is None or maskName is None:  # Something went wrong, in this case PyRadiomics will also log an error\n",
+    "if imagePath is None or maskPath is None:  # Something went wrong, in this case PyRadiomics will also log an error\n",
     "    print('Error getting testcase!')\n",
     "\n",
-    "# Additonally, store the location of the example parameter file, stored in \\pyradiomics\\bin\n",
-    "paramPath = os.path.join(os.getcwd(), \"..\", \"Params.yaml\")\n",
+    "# Additonally, store the location of the example parameter file, stored in \\pyradiomics\\examples/exampleSettings\n",
+    "paramPath = os.path.join(os.getcwd(), \"..\", \"exampleSettings\", \"Params.yaml\")\n",
     "print(\"Parameter file, absolute path:\", os.path.abspath(paramPath))"
    ]
   },

diff --git a/bin/Notebooks/RadiomicsExample.ipynb → examples/Notebooks/RadiomicsExample.ipynb b/bin/Notebooks/RadiomicsExample.ipynb → examples/Notebooks/RadiomicsExample.ipynb
diff --git a/bin/Notebooks/helloFeatureClass.ipynb → examples/Notebooks/helloFeatureClass.ipynb b/bin/Notebooks/helloFeatureClass.ipynb → examples/Notebooks/helloFeatureClass.ipynb
diff --git a/bin/Notebooks/helloRadiomics.ipynb → examples/Notebooks/helloRadiomics.ipynb b/bin/Notebooks/helloRadiomics.ipynb → examples/Notebooks/helloRadiomics.ipynb
diff --git a/bin/batchExamples/DatasetHierarchyReader.py → ...s/batchExamples/DatasetHierarchyReader.py b/bin/batchExamples/DatasetHierarchyReader.py → ...s/batchExamples/DatasetHierarchyReader.py
diff --git a/...ples/GenerateInputCSV_Datasethierarchy.py → ...ples/GenerateInputCSV_Datasethierarchy.py b/...ples/GenerateInputCSV_Datasethierarchy.py → ...ples/GenerateInputCSV_Datasethierarchy.py
diff --git a/...atchExamples/GenerateInputCSV_Filename.py → ...atchExamples/GenerateInputCSV_Filename.py b/...atchExamples/GenerateInputCSV_Filename.py → ...atchExamples/GenerateInputCSV_Filename.py
diff --git a/bin/batchExamples/batchProcessingPandas.py → ...es/batchExamples/batchProcessingPandas.py b/bin/batchExamples/batchProcessingPandas.py → ...es/batchExamples/batchProcessingPandas.py
diff --git a/bin/batchExamples/batchprocessing.py → examples/batchExamples/batchprocessing.py b/bin/batchExamples/batchprocessing.py → examples/batchExamples/batchprocessing.py
diff --git a/bin/Params.yaml → examples/exampleSettings/Params.yaml b/bin/Params.yaml → examples/exampleSettings/Params.yaml
diff --git a/bin/helloFeatureClass.py → examples/helloFeatureClass.py b/bin/helloFeatureClass.py → examples/helloFeatureClass.py
diff --git a/bin/helloRadiomics.py → examples/helloRadiomics.py b/bin/helloRadiomics.py → examples/helloRadiomics.py
diff --git a/bin/helloResampling.py → examples/helloResampling.py b/bin/helloResampling.py → examples/helloResampling.py
diff --git a/radiomics/shape.py b/radiomics/shape.py
@@ -233,8 +233,8 @@ def getSphericityFeatureValue(self):
     .. note::
 
       This feature is correlated to Compactness 1, Compactness 2 and Spherical Disproportion. In the default
-      parameter file provided in the ``pyradiomics\bin`` folder, Compactness 1 and Compactness 2 are therefore
-      disabled.
+      parameter file provided in the ``pyradiomics/examples/exampleSettings`` folder, Compactness 1 and Compactness 2
+      are therefore disabled.
     """
     return (36 * numpy.pi * self.Volume ** 2) ** (1.0 / 3.0) / self.SurfaceArea
 
@@ -257,8 +257,8 @@ def getCompactness1FeatureValue(self):
     .. note::
 
       This feature is correlated to Compactness 2, Sphericity and Spherical Disproportion. In the default
-      parameter file provided in the ``pyradiomics\bin`` folder, Compactness 1 and Compactness 2 are therefore
-      disabled.
+      parameter file provided in the ``pyradiomics/examples/exampleSettings`` folder, Compactness 1 and Compactness 2
+      are therefore disabled.
     """
     return ((self.Volume) / ((self.SurfaceArea) ** (3.0 / 2.0) * numpy.sqrt(numpy.pi)))
 
@@ -279,8 +279,8 @@ def getCompactness2FeatureValue(self):
     .. note::
 
       This feature is correlated to Compactness 1, Sphericity and Spherical Disproportion. In the default
-      parameter file provided in the ``pyradiomics\bin`` folder, Compactness 1 and Compactness 2 are therefore
-      disabled.
+      parameter file provided in the ``pyradiomics/examples/exampleSettings`` folder, Compactness 1 and Compactness 2
+      are therefore disabled.
     """
     return ((36.0 * numpy.pi) * ((self.Volume) ** 2.0) / ((self.SurfaceArea) ** 3.0))
 
@@ -301,9 +301,9 @@ def getSphericalDisproportionFeatureValue(self):
 
     .. note::
 
-      This feature is correlated to Compactness 1, Sphericity and Spherical Disproportion. In the default
-      parameter file provided in the ``pyradiomics\bin`` folder, Compactness 1 and Compactness 2 are therefore
-      disabled.
+      This feature is correlated to Compactness 1, Compactness 2 and Sphericity. In the default
+      parameter file provided in the ``pyradiomics/examples/exampleSettings`` folder, Compactness 1 and Compactness 2
+      are therefore disabled.
     """
     return self.SurfaceArea / (36 * numpy.pi * self.Volume ** 2) ** (1.0 / 3.0)