Merge pull request #207 from JoostJM/Update-README

Update readme

README.md

@@ -5,7 +5,7 @@
 
 [![Travis CI](https://travis-ci.org/Radiomics/pyradiomics.svg?branch=master)](https://travis-ci.org/Radiomics/pyradiomics)
 
-# pyradiomics v1.0
+# pyradiomics v1.1.0
 
 ## Radiomics feature extraction in Python
 
@@ -54,10 +54,14 @@ Furthermore, an instruction video is available [here](http://radiomics.io/pyradi
 
 ### Installation
 
-To install this package run the following commands from the root directory:
+PyRadiomics is OS independent and compatible with both Python 2.7 and Python >=3.4.
+To install this package on unix like systems run the following commands from the root directory:
 
-    python -m pip install -r requirements.txt
-    python setup.py install
+    sudo python -m pip install -r requirements.txt
+    sudo python setup.py install
+
+Detailed installation instructions, as well as instructions for installing PyRadiomics on Windows are available in the 
+[documentation](http://pyradiomics.readthedocs.io/en/latest/installation.html).
 
 ### Usage
 
@@ -87,7 +91,6 @@ See also the [requirements file](requirements.txt).
 
 ### WIP
  - Implementation of this package as an [extension](https://github.com/Radiomics/SlicerRadiomics) to [3D Slicer](slicer.org)
- - Enhancing performance by implementation of C for computationally expensive code
 
 ### License
 This package is covered by the [3D Slicer License](LICENSE.txt).

bin/Notebooks/helloRadiomics.ipynb

@@ -154,25 +154,25 @@
      "output_type": "stream",
      "text": [
       "Enabled input images:\n",
-      "\toriginal\n"
+      "\tOriginal\n"
      ]
     }
    ],
    "source": [
     "# By default, only 'original' (no filter applied) is enabled. Optionally enable some filters:\n",
     "\n",
-    "# extractor.enableInputImageByName('wavelet')\n",
-    "# extractor.enableInputImageByName('log', customArgs={'sigma':[3.0]})\n",
-    "# extractor.enableInputImageByName('square')\n",
-    "# extractor.enableInputImageByName('squareroot')\n",
-    "# extractor.enableInputImageByName('exponential')\n",
-    "# extractor.enableInputImageByName('logarithm')\n",
+    "# extractor.enableInputImageByName('Wavelet')\n",
+    "# extractor.enableInputImageByName('LoG', customArgs={'sigma':[3.0]})\n",
+    "# extractor.enableInputImageByName('Square')\n",
+    "# extractor.enableInputImageByName('SquareRoot')\n",
+    "# extractor.enableInputImageByName('Exponential')\n",
+    "# extractor.enableInputImageByName('Logarithm')\n",
     "\n",
     "# Alternative; set filters in one operation \n",
     "# This updates current enabled input images, i.e. overwrites custom settings. \n",
     "# However, input images already enabled, but not passed in this call, are not disabled.\n",
     "\n",
-    "# extractor.enableInputImages(wavelet={}, log={'sigma':[3.0]})\n",
+    "# extractor.enableInputImages(Wavelet={}, LoG={'sigma':[3.0]})\n",
     "\n",
     "print(\"Enabled input images:\")\n",
     "for imageType in extractor.inputImages.keys():\n",
@@ -248,6 +248,7 @@
       "\n",
       "    :math:`entropy = -\\displaystyle\\sum^{N_l}_{i=1}{p(i)\\log_2\\big(p(i)+\\epsilon\\big)}`\n",
       "\n",
+      "    Here, :math:`\\epsilon` is an arbitrarily small positive number (:math:`\\approx 2.2\\times10^{-16}`).\n",
       "    Entropy specifies the uncertainty/randomness in the\n",
       "    image values. It measures the average amount of\n",
       "    information required to encode the image values.\n",
@@ -423,12 +424,12 @@
       "Calculating features\n",
       "\t\tComputing firstorder\n",
       "Computed general_info_BoundingBox: (162; 84; 11; 47; 70; 7)\n",
-      "Computed general_info_GeneralSettings: {'verbose': True; 'binWidth': 25; 'label': 1; 'interpolator': 'sitkBSpline'; 'resampledPixelSpacing': None; 'padDistance': 5}\n",
+      "Computed general_info_GeneralSettings: {'additionalInfo': True; 'verbose': True; 'binWidth': 25; 'enableCExtensions': True; 'label': 1; 'interpolator': 'sitkBSpline'; 'resampledPixelSpacing': None; 'padDistance': 5}\n",
       "Computed general_info_ImageHash: 5c9ce3ca174f0f8324aa4d277e0fef82dc5ac566\n",
       "Computed general_info_ImageSpacing: (0.7812499999999999; 0.7812499999999999; 6.499999999999998)\n",
-      "Computed general_info_InputImages: {'original': {}}\n",
+      "Computed general_info_InputImages: {'Original': {}}\n",
       "Computed general_info_MaskHash: 9dc2c3137b31fd872997d92c9a92d5178126d9d3\n",
-      "Computed general_info_Version: v1.0.post11.dev0+g610dffc\n",
+      "Computed general_info_Version: v1.0.1.post69.dev0+gc00bfe2\n",
       "Computed general_info_VolumeNum: 2\n",
       "Computed general_info_VoxelNum: 4137\n",
       "Computed original_firstorder_InterquartileRange: 253.0\n",
@@ -471,7 +472,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 2
+    "version": 2.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -483,4 +484,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}

bin/batchExamples/batchprocessing.py

@@ -56,12 +56,13 @@ def main():
   kwargs['resampledPixelSpacing'] = None  # [3,3,3]
   kwargs['interpolator'] = sitk.sitkBSpline
   kwargs['verbose'] = True
+  kwargs['enableCExtensions'] = False
 
   logging.info('pyradiomics version: %s', radiomics.__version__)
   logging.info('Extracting features with kwarg settings: %s', str(kwargs))
 
   extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)
-  extractor.enableInputImages(original={})
+  extractor.enableInputImages(Original={})
   # extractor.enableInputImages(wavelet= {'level': 2})
   for idx, entry in enumerate(flists, start=1):
 

bin/helloFeatureClass.py

@@ -149,7 +149,7 @@
 #
 if applyLog:
   sigmaValues = numpy.arange(5., 0., -.5)[::1]
-  for logImage, inputImageName, inputKwargs in imageoperations.applyFilterLoG(image, sigma=sigmaValues, verbose=True):
+  for logImage, inputImageName, inputKwargs in imageoperations.getLoGImage(image, sigma=sigmaValues, verbose=True):
     logFirstorderFeatures = firstorder.RadiomicsFirstOrder(logImage, mask, **inputKwargs)
     logFirstorderFeatures.enableAllFeatures()
     logFirstorderFeatures.calculateFeatures()
@@ -160,7 +160,7 @@
 # Show FirstOrder features, calculated on a wavelet filtered image
 #
 if applyWavelet:
-  for decompositionImage, decompositionName, inputKwargs in imageoperations.applyFilterWavelet(image):
+  for decompositionImage, decompositionName, inputKwargs in imageoperations.getWaveletImage(image):
     waveletFirstOrderFeaturs = firstorder.RadiomicsFirstOrder(decompositionImage, mask, **inputKwargs)
     waveletFirstOrderFeaturs.enableAllFeatures()
     waveletFirstOrderFeaturs.calculateFeatures()

docs/index.rst

@@ -65,17 +65,20 @@ Joost J.M. van Griethuysen et al, “Computational Radiomics System to Decode th
 Installation
 ------------
 
+PyRadiomics is OS independent and compatible with both Python 2.7 and Python >=3.4.
+
 * Clone the repository
 
   * ``git clone git://github.com/Radiomics/pyradiomics``
 
-* Install on your system, with prerequisites:
+* Install on your system (Linux, Mac OSX), with prerequisites:
 
   * ``cd pyradiomics``
   * ``sudo python -m pip install -r requirements.txt``
   * ``sudo python setup.py install``
 
-* For more detailed installation instructions see :ref:`Installation Details<installation-label>`
+* For more detailed installation instructions and installation on Windows see
+  :ref:`Installation Details<installation-label>`
 
 .. toctree::
    :maxdepth: 2

docs/installation.rst

@@ -8,7 +8,7 @@ Get the code
 
 * Ensure you have the version control system ``git`` installed on your machine.
 
-* Ensure that you have ``python`` installed on your machine, at least version 2.7.
+* Ensure that you have ``python`` installed on your machine, at least version 2.7 or 3.4.
 
 * Clone the repository:
 

docs/usage.rst

@@ -98,6 +98,7 @@ Interactive Use
 * Import the necessary classes::
 
      from radiomics import featureextractor
+     import six
      import sys, os
 
 * Set up a pyradiomics directory variable::
@@ -153,6 +154,7 @@ Using feature classes directly
 
      from radiomics import firstorder, glcm, imageoperations, shape, glrlm, glszm
      import SimpleITK as sitk
+     import six
      import sys, os
 
 * Set up a data directory variable::

setup.py

@@ -88,6 +88,8 @@ def run_tests(self):
         'Programming Language :: C',
         'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
     ],