ENH: Pass in the class instance to the PyImageFilter PyGenerateData

It was difficult or not possible to write a useful PyGenerateData
function without access to the calling filter. Pass the filter in as an
argument to the callable.

Fix an issue where Modified() was not called if a new function was not
added.

Add tests.

Wrapping/Generators/Python/CMakeLists.txt

@@ -770,6 +770,9 @@ macro(itk_wrap_simple_type_python wrap_class swig_name)
     set(ITK_WRAP_PYTHON_SWIG_EXT "${ITK_WRAP_PYTHON_SWIG_EXT}DECL_PYTHON_IMAGE_CLASS(${swig_name})\n\n")
   endif()
 
+  if("${cpp_name}" STREQUAL "itk::PyImageFilter" AND NOT "${swig_name}" MATCHES "Pointer$")
+    set(ITK_WRAP_PYTHON_SWIG_EXT "${ITK_WRAP_PYTHON_SWIG_EXT}DECL_PYIMAGEFILTER_CLASS(${swig_name})\n\n")
+  endif()
 
   if("${cpp_name}" STREQUAL "itk::StatisticsLabelObject" AND NOT "${swig_name}" MATCHES "Pointer$")
     set(ITK_WRAP_PYTHON_SWIG_EXT "${ITK_WRAP_PYTHON_SWIG_EXT}%template(map${swig_name}) std::map< unsigned long, ${swig_name}_Pointer, std::less< unsigned long > >;\n")

Wrapping/Generators/Python/PyBase/pyBase.i

@@ -189,6 +189,20 @@ str = str
 //    $1 = ptr;
 //    }
 
+%define DECL_PYIMAGEFILTER_CLASS(swig_name)
+    %extend swig_name {
+        %pythoncode {
+            def Update(self):
+                """Internal method to pass a pointer to the Python object wrapper, then call Update() on the filter."""
+                self._SetSelf(self)
+                super().Update()
+            def UpdateLargestPossibleRegion(self):
+                """Internal method to pass a pointer to the Python object wrapper, then call UpdateLargestPossibleRegion() on the filter."""
+                self._SetSelf(self)
+                super().UpdateLargestPossibleRegion()
+        }
+    }
+%enddef
 
 %extend itkComponentTreeNode {
     %pythoncode {

Wrapping/Generators/Python/PyUtils/itkPyImageFilter.h

@@ -30,11 +30,12 @@ namespace itk
 {
 
 /** \class PyImageFilter
- *  \brief ImageToImageFilter subclass that calls a Python callable object, e.g.
- *  a Python function.
+ * \brief ImageToImageFilter subclass that calls a Python callable object, e.g.
+ * a Python function or a class with a __call__ method.
+ *
+ * For more information on ITK filters, the GenerateData() method, and other filter pipeline methods,
+ * see the ITK Software Guide.
  */
-
-
 template <class TInputImage, class TOutputImage>
 class ITK_TEMPLATE_EXPORT PyImageFilter : public ImageToImageFilter<TInputImage, TOutputImage>
 {
@@ -67,18 +68,26 @@ class ITK_TEMPLATE_EXPORT PyImageFilter : public ImageToImageFilter<TInputImage,
   static constexpr unsigned int InputImageDimension = TInputImage::ImageDimension;
   static constexpr unsigned int OutputImageDimension = TOutputImage::ImageDimension;
 
-
+  /** Python callable called during the filter's GenerateData. */
   void
   SetPyGenerateData(PyObject * obj);
 
+  /** Python internal method to pass a pointer to the wrapping Python object. */
+  void
+  _SetSelf(PyObject * self)
+  {
+    this->m_Self = self;
+  }
+
 protected:
   PyImageFilter();
   virtual ~PyImageFilter();
-  virtual void
-  GenerateData();
+  void
+  GenerateData() override;
 
 private:
-  PyObject * m_Object;
+  PyObject * m_Self;
+  PyObject * m_GenerateDataCallable;
 };
 
 } // end namespace itk

Wrapping/Generators/Python/PyUtils/itkPyImageFilter.hxx

@@ -26,39 +26,40 @@ namespace itk
 template <class TInputImage, class TOutputImage>
 PyImageFilter<TInputImage, TOutputImage>::PyImageFilter()
 {
-  this->m_Object = nullptr;
+  this->m_GenerateDataCallable = nullptr;
 }
 
 template <class TInputImage, class TOutputImage>
 PyImageFilter<TInputImage, TOutputImage>::~PyImageFilter()
 {
-  if (this->m_Object)
+  if (this->m_GenerateDataCallable)
   {
-    Py_DECREF(this->m_Object);
+    Py_DECREF(this->m_GenerateDataCallable);
   }
-  this->m_Object = nullptr;
+  this->m_GenerateDataCallable = nullptr;
 }
 
 template <class TInputImage, class TOutputImage>
 void
 PyImageFilter<TInputImage, TOutputImage>::SetPyGenerateData(PyObject * o)
 {
-  if (o != this->m_Object)
+  if (o != this->m_GenerateDataCallable)
   {
-    if (this->m_Object)
+    if (this->m_GenerateDataCallable)
     {
       // get rid of our reference
-      Py_DECREF(this->m_Object);
+      Py_DECREF(this->m_GenerateDataCallable);
     }
 
     // store the new object
-    this->m_Object = o;
+    this->m_GenerateDataCallable = o;
+    this->Modified();
 
-    if (this->m_Object)
+    if (this->m_GenerateDataCallable)
     {
       // take out reference (so that the calling code doesn't
       // have to keep a binding to the callable around)
-      Py_INCREF(this->m_Object);
+      Py_INCREF(this->m_GenerateDataCallable);
     }
   }
 }
@@ -69,7 +70,7 @@ void
 PyImageFilter<TInputImage, TOutputImage>::GenerateData()
 {
   // make sure that the CommandCallable is in fact callable
-  if (!PyCallable_Check(this->m_Object))
+  if (!PyCallable_Check(this->m_GenerateDataCallable))
   {
     // we throw a standard ITK exception: this makes it possible for
     // our standard Swig exception handling logic to take this
@@ -81,7 +82,9 @@ PyImageFilter<TInputImage, TOutputImage>::GenerateData()
   {
     PyObject * result;
 
-    result = PyEval_CallObject(this->m_Object, (PyObject *)nullptr);
+    PyObject * args = PyTuple_Pack(1, this->m_Self);
+    result = PyObject_Call(this->m_GenerateDataCallable, args, (PyObject *)NULL);
+    Py_DECREF(args);
 
     if (result)
     {

Wrapping/Generators/Python/Tests/CMakeLists.txt

@@ -24,6 +24,7 @@ itk_python_add_test(NAME PythonDICOMSeries COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/d
               DATA{${ITK_DATA_ROOT}/Input/DicomSeries/Image0075.dcm}
               DATA{${ITK_DATA_ROOT}/Input/DicomSeries/Image0076.dcm}
               DATA{${ITK_DATA_ROOT}/Input/DicomSeries/Image0077.dcm})
+itk_python_add_test(NAME PyImageFilterTest COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/PyImageFilterTest.py)
 
 # some tests will fail if dim=2 and unsigned short are not wrapped
 INTERSECTION(WRAP_2 2 "${ITK_WRAP_IMAGE_DIMS}")

Wrapping/Generators/Python/Tests/PyImageFilterTest.py

@@ -0,0 +1,53 @@
+# ==========================================================================
+#
+#   Copyright NumFOCUS
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#          http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+# ==========================================================================*/
+
+import itk
+import numpy as np
+import functools
+
+input_image = itk.image_from_array(np.random.randint(0,255,size=(6,6), dtype=np.uint8))
+
+py_filter = itk.PyImageFilter.New(input_image)
+
+def constant_wrapper(f, constant=42):
+    @functools.wraps(f)
+    def wrapper(*args):
+        return f(*args, constant=constant)
+    return wrapper
+
+def constant_output(py_image_filter, constant=42):
+    output = py_image_filter.GetOutput()
+    output.SetBufferedRegion(output.GetRequestedRegion())
+    output.Allocate()
+    output.FillBuffer(constant)
+
+py_filter.SetPyGenerateData(constant_output)
+py_filter.Update()
+output_image = py_filter.GetOutput()
+assert np.all(np.asarray(output_image) == 42)
+
+# Filter calls Modified because a new PyGenerateData was passed
+py_filter.SetPyGenerateData(constant_wrapper(constant_output, 10))
+py_filter.Update()
+output_image = py_filter.GetOutput()
+assert np.all(np.asarray(output_image) == 10)
+
+# Functional interface
+output_image = itk.py_image_filter(input_image,
+                                   py_generate_data=constant_wrapper(constant_output, 7))
+assert np.all(np.asarray(output_image) == 7)