ENH: Update Bridge Numpy (2016.12.05)

Francois Budin (3):
      BUG: Wrap RGB, RGBA, and Vector images types
      ENH: Adding test for ITK images with RGB/RGBA/Vector pixels
      ENH: Adding conversion from VNL objects to Numpy objects

Matt McCormick (3):
      Merge pull request InsightSoftwareConsortium#9 from fbudin69500/WrapRGBRGBAVectorImages
      Merge pull request InsightSoftwareConsortium#10 from fbudin69500/Add_tests_for_RGB_RGBA_Vector_images
      Merge pull request InsightSoftwareConsortium#11 from fbudin69500/numpy_vnl_objects

Diff:
InsightSoftwareConsortium/ITKBridgeNumPy@9b5b17a...ab8df8c

Change-Id: Iffd201bb5b438cac64199bc969ba9b4ae44816e2

Modules/Remote/BridgeNumPy.remote.cmake

@@ -9,8 +9,17 @@ itk_fetch_module(BridgeNumPy
     array = itk.PyBuffer[ImageType].GetArrayFromImage(image)
     image = itk.PyBuffer[ImageType].GetImageFromArray(array)
 
+  It also enables conversion of a VNL vector or matrix into a NumPy array and
+  back. For example:
+
+    import itk
+    v = itk.vnl_vector[itk.F]()
+    v.set_size(2)
+    arr = itk.PyVnl[itk.F].GetArrayFromVnlVector(v)
+    v = itk.PyVnl[itk.F].GetVnlVectorFromArray(arr)
+
   See http://insight-journal.org/browse/publication/85
       https://hdl.handle.net/1926/188"
   GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKBridgeNumPy.git
-  GIT_TAG 9b5b17a462e88478f3ea780b805b6a3a5e10dee5
+  GIT_TAG ab8df8c1c8494416d5c8471382413c49c9163d9b
   )

Utilities/Maintenance/BuildHeaderTest.py

@@ -40,6 +40,7 @@
     'itkFFTWComplexToComplexFFTImageFilter.h',
     'itkFFTWCommon.h',
     'itkPyBuffer.h', # needs Python.h, etc
+    'itkPyVnl.h', # needs Python.h, etc
     'itkVanHerkGilWermanErodeDilateImageFilter.h', # circular include's
     'itkBSplineDeformableTransform.h',   # deprecated
     'vtkCaptureScreen.h',  # these includes require VTK

Wrapping/Generators/Python/itkExtras.py

@@ -259,6 +259,53 @@ def GetImageFromArray(arr):
     ImageType = itk.Image[PixelType,arr.ndim]
     return itk.PyBuffer[ImageType].GetImageFromArray(arr)
 
+def GetArrayFromVnlVector(vnlVector):
+    """Get an Array with the content of the vnlVector
+    """
+    # Check for numpy
+    if not HAVE_NUMPY:
+        raise ImportError('Numpy not available.')
+    # Finds the vnl vector type
+    import itk
+    VectorPixelType = itk.template(vnlVector)[1][0]
+    keys = [k for k in itk.PyVnl.keys() if k[0] == VectorPixelType]
+    if len(keys ) == 0:
+        raise RuntimeError("No suitable template parameter can be found.")
+    # Create a numpy array of the type of the vnl vector
+    return itk.PyVnl[keys[0]].GetArrayFromVnlVector(vnlVector)
+
+def GetVnlVectorFromArray(arr):
+    """Get a vnl vector from a Python array.
+    """
+    if not HAVE_NUMPY:
+        raise ImportError('Numpy not available.')
+    import itk
+    PixelType = _get_itk_pixelid(arr)
+    return itk.PyVnl[PixelType].GetVnlVectorFromArray(arr)
+
+def GetArrayFromVnlMatrix(vnlMatrix):
+    """Get an Array with the content of the vnl matrix
+    """
+    # Check for numpy
+    if not HAVE_NUMPY:
+        raise ImportError('Numpy not available.')
+    # Finds the vnl matrix type
+    import itk
+    PixelType = itk.template(vnlMatrix)[1][0]
+    keys = [k for k in itk.PyVnl.keys() if k[0] == PixelType]
+    if len(keys ) == 0:
+        raise RuntimeError("No suitable template parameter can be found.")
+    # Create a numpy array of the type of the vnl matrix
+    return itk.PyVnl[keys[0]].GetArrayFromVnlMatrix(vnlMatrix)
+
+def GetVnlMatrixFromArray(arr):
+    """Get a vnl matrix from a Python array.
+    """
+    if not HAVE_NUMPY:
+        raise ImportError('Numpy not available.')
+    import itk
+    PixelType = _get_itk_pixelid(arr)
+    return itk.PyVnl[PixelType].GetVnlMatrixFromArray(arr)
 
 # return an image
 from itkTemplate import image, output