BUG: Specify itk package in SWIG Python modules

This consistently sets the __package__ for `itk` package modules and functions. This addresses Windows import failures. Swig's c-module import statements changed with Swig 4.0. For the new syntax, __package__ must be set and consistent on the imported modules. To simplify things, Linux and macOS are also updated to Swig 4.0. itk.FloatingPointExceptions, itk.AdaptiveHistogramEqualizationImageFilter is disabled because it on macOs, Linux with Swig 4.0.1. The library outputs in the build tree are changed to be consistent with the package layout. We use the standard API for ImageDuplicator invocation in the NumPy bridge. For the embedded submodules on the C side, we update the module name to include `itk.` We also use a single PyImport_GetModuleDict statement for simplicity and performance. For imports of submodules in Python, we now use the full path. The "swig" attribute is now a dict used as a namespace instead of a types.ModuleType. Overriding the `.New()` is moved from pyBase.i to igenerator.py. It is only added to classes that define a .New() and have .AddObserver(), i.e. not abstract base classes. itk.PyCommand is excluded to prevent .AddObserver recursion that blows the stack. The lazy module creation uses Python 3.5 tooling to create a module with __package__ set and load it lazily. i.e. importlib.util.spec_from_file_location importlib.util.module_from_spec module.__loader__.exec_module Loaded modules now have the package path in their name.
InsightSoftwareConsortium · May 25, 2020 · 98fc085 · 98fc085
1 parent 1ab2baa
commit 98fc085
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Showing 16 changed files with 197 additions and 141 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -257,7 +257,11 @@ if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${ITK_BINARY_DIR}/bin)
 endif()
 if(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
-  set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${ITK_BINARY_DIR}/lib)
+  if(ITK_WRAP_PYTHON)
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${ITK_BINARY_DIR}/Wrapping/Generators/Python/itk)
+  else()
+    set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${ITK_BINARY_DIR}/lib)
+  endif()
 endif()
 if(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
   set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${ITK_BINARY_DIR}/lib)

diff --git a/Modules/Bridge/NumPy/wrapping/PyBuffer.i.in b/Modules/Bridge/NumPy/wrapping/PyBuffer.i.in
@@ -125,8 +125,8 @@
         imageView = itkPyBuffer@[email protected](ndarr, is_vector)
 
         # Duplicate the image to let it manage its own memory buffer
-        duplicator = itkImageDuplicator@[email protected]()
-        duplicator.SetInputImage(imageView)
+        import itk
+        duplicator = itk.ImageDuplicator.New(imageView)
         duplicator.Update()
         return duplicator.GetOutput()
 

diff --git a/Modules/Bridge/NumPy/wrapping/PyBuffer.i.init b/Modules/Bridge/NumPy/wrapping/PyBuffer.i.init
@@ -43,6 +43,4 @@ def _get_numpy_pixelid(itk_Image_type):
         return _np_itk[itk_Image_type]
     except KeyError as e:
         raise e
-
-from itkImageDuplicatorPython import *
 %}
diff --git a/Modules/Bridge/VtkGlue/wrapping/VtkGlue.i b/Modules/Bridge/VtkGlue/wrapping/VtkGlue.i
@@ -48,7 +48,7 @@
 #endif
 
 #ifdef SWIGPYTHON
-%module VtkGluePython
+%module(package=\"itk\",threads=\"1\") VtkGluePython
 
 %{
 #include "vtkPythonUtil.h"

diff --git a/Modules/Core/Common/wrapping/itkFloatingPointExceptions.wrap b/Modules/Core/Common/wrapping/itkFloatingPointExceptions.wrap
@@ -1,4 +1,4 @@
 set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
 itk_wrap_include("itkFloatingPointExceptions.h")
-itk_wrap_simple_class("itk::FloatingPointExceptions")
-itk_wrap_simple_class("itk::FloatingPointExceptionsEnums")
+#itk_wrap_simple_class("itk::FloatingPointExceptions")
+#itk_wrap_simple_class("itk::FloatingPointExceptionsEnums")
diff --git a/Modules/Filtering/ImageStatistics/wrapping/itkAdaptiveHistogramEqualizationImageFilter.wrap b/Modules/Filtering/ImageStatistics/wrapping/itkAdaptiveHistogramEqualizationImageFilter.wrap
@@ -1,36 +1,36 @@
-itk_wrap_class("itk::KernelImageFilter" POINTER)
-  foreach(t ${WRAP_ITK_SCALAR})
-    foreach(d ${ITK_WRAP_IMAGE_DIMS})
-      itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}Neighborhood" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >")
-    endforeach()
-  endforeach()
-itk_end_wrap_class()
+#itk_wrap_class("itk::KernelImageFilter" POINTER)
+  #foreach(t ${WRAP_ITK_SCALAR})
+    #foreach(d ${ITK_WRAP_IMAGE_DIMS})
+      #itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}Neighborhood" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >")
+    #endforeach()
+  #endforeach()
+#itk_end_wrap_class()
 
-itk_wrap_class("itk::MovingHistogramImageFilterBase" POINTER)
-  foreach(t ${WRAP_ITK_SCALAR})
-    foreach(d ${ITK_WRAP_IMAGE_DIMS})
-      itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}Neighborhood" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >")
-    endforeach()
-  endforeach()
-itk_end_wrap_class()
+#itk_wrap_class("itk::MovingHistogramImageFilterBase" POINTER)
+  #foreach(t ${WRAP_ITK_SCALAR})
+    #foreach(d ${ITK_WRAP_IMAGE_DIMS})
+      #itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}Neighborhood" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >")
+    #endforeach()
+  #endforeach()
+#itk_end_wrap_class()
 
-set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
-itk_wrap_include("itkAdaptiveEqualizationHistogram.h")
-itk_wrap_class("itk::Function::AdaptiveEqualizationHistogram")
-  foreach(t ${WRAP_ITK_SCALAR})
-    itk_wrap_template("${ITKM_${t}}${ITKM_${t}}" "${ITKT_${t}}, ${ITKT_${t}}")
-  endforeach()
-itk_end_wrap_class()
-set(WRAPPER_AUTO_INCLUDE_HEADERS ON)
+#set(WRAPPER_AUTO_INCLUDE_HEADERS OFF)
+#itk_wrap_include("itkAdaptiveEqualizationHistogram.h")
+#itk_wrap_class("itk::Function::AdaptiveEqualizationHistogram")
+  #foreach(t ${WRAP_ITK_SCALAR})
+    #itk_wrap_template("${ITKM_${t}}${ITKM_${t}}" "${ITKT_${t}}, ${ITKT_${t}}")
+  #endforeach()
+#itk_end_wrap_class()
+#set(WRAPPER_AUTO_INCLUDE_HEADERS ON)
 
-itk_wrap_class("itk::MovingHistogramImageFilter" POINTER)
-  foreach(t ${WRAP_ITK_SCALAR})
-    foreach(d ${ITK_WRAP_IMAGE_DIMS})
-      itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}NeighborhoodAHE" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >, itk::Function::AdaptiveEqualizationHistogram< ${ITKT_${t}}, ${ITKT_${t}} >")
-    endforeach()
-  endforeach()
-itk_end_wrap_class()
+#itk_wrap_class("itk::MovingHistogramImageFilter" POINTER)
+  #foreach(t ${WRAP_ITK_SCALAR})
+    #foreach(d ${ITK_WRAP_IMAGE_DIMS})
+      #itk_wrap_template("${ITKM_I${t}${d}}${ITKM_I${t}${d}}NeighborhoodAHE" "${ITKT_I${t}${d}}, ${ITKT_I${t}${d}}, itk::Neighborhood< bool, ${d} >, itk::Function::AdaptiveEqualizationHistogram< ${ITKT_${t}}, ${ITKT_${t}} >")
+    #endforeach()
+  #endforeach()
+#itk_end_wrap_class()
 
-itk_wrap_class("itk::AdaptiveHistogramEqualizationImageFilter" POINTER)
-  itk_wrap_image_filter("${WRAP_ITK_SCALAR}" 1)
-itk_end_wrap_class()
+#itk_wrap_class("itk::AdaptiveHistogramEqualizationImageFilter" POINTER)
+  #itk_wrap_image_filter("${WRAP_ITK_SCALAR}" 1)
+#itk_end_wrap_class()
diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt
@@ -230,7 +230,8 @@ macro(itk_wrap_module_python library_name)
   set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "")
   set(ITK_WRAP_PYTHON_LIBRARY_DEPS )
   set(ITK_WRAP_PYTHON_LIBRARY_DECLS )
-  set(ITK_WRAP_PYTHON_LIBRARY_CALLS )
+  set(ITK_WRAP_PYTHON_LIBRARY_CALLS "
+  PyObject * sysModules = PyImport_GetModuleDict();\n")
   set(ITK_WRAP_PYTHON_CXX_FILES )
   if(MSVC)
     get_filename_component(python_library_directory "${Python3_LIBRARY}" DIRECTORY)
@@ -343,13 +344,13 @@ macro(itk_end_wrap_module_python)
 
   foreach(dep ${WRAPPER_LIBRARY_DEPENDS})
     set(ITK_WRAP_PYTHON_CONFIGURATION_DEPENDS "'${dep}', ${ITK_WRAP_PYTHON_CONFIGURATION_DEPENDS}")
-    set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "import ${dep}Python\n${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}")
+    set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "import itk.${dep}Python\n${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}")
   endforeach()
 
   # ITKPyBase is always included, excepted ITKPyBase itself
   if(NOT "${WRAPPER_LIBRARY_NAME}" STREQUAL "ITKPyBase")
     set(ITK_WRAP_PYTHON_CONFIGURATION_DEPENDS "'ITKPyBase', ${ITK_WRAP_PYTHON_CONFIGURATION_DEPENDS}")
-    set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "import ITKPyBasePython\n${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}")
+    set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "import itk.ITKPyBasePython\n${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}")
   endif()
 
   # and create the file, with the var ITK_WRAP_PYTHON_CONFIGURATION_TEMPLATES and
@@ -580,13 +581,12 @@ macro(itk_end_wrap_submodule_python group_name)
   # first the extern c declaration and then the call of the extern function
   set(ITK_WRAP_PYTHON_LIBRARY_DECLS "${ITK_WRAP_PYTHON_LIBRARY_DECLS} extern \"C\" PyMODINIT_FUNC PyInit__${group_name}Python();\n")
   set(ITK_WRAP_PYTHON_LIBRARY_CALLS "${ITK_WRAP_PYTHON_LIBRARY_CALLS}
-  PyObject * ${group_name}SysModules = PyImport_GetModuleDict();
-  PyObject * ${group_name}AlreadyImported = PyDict_GetItemString(${group_name}SysModules, \"_${group_name}Python\");
+  PyObject * ${group_name}AlreadyImported = PyDict_GetItemString(sysModules, \"itk._${group_name}Python\");
   if( ${group_name}AlreadyImported == NULL )
     {
-    PyImport_AddModule( \"_${group_name}Python\" );
+    PyImport_AddModule( \"itk._${group_name}Python\" );
     PyObject * ${group_name}Module = PyInit__${group_name}Python();
-    PyDict_SetItemString( ${group_name}SysModules, \"_${group_name}Python\", ${group_name}Module );
+    PyDict_SetItemString( sysModules, \"itk._${group_name}Python\", ${group_name}Module );
     Py_DECREF( ${group_name}Module );
     }
 ")
@@ -627,7 +627,7 @@ macro(itk_wrap_submodule_python module)
   set(ITK_WRAP_PYTHON_SWIG_EXT "\n")
 
   # register the module for the lib module
-  set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}from ${module}Python import *\n")
+  set(ITK_WRAP_PYTHON_LIBRARY_IMPORTS "${ITK_WRAP_PYTHON_LIBRARY_IMPORTS}from itk.${module}Python import *\n")
 
 endmacro()
 

diff --git a/Wrapping/Generators/Python/PyBase/pyBase.i b/Wrapping/Generators/Python/PyBase/pyBase.i
@@ -1,4 +1,4 @@
-%module pyBasePython
+%module(package="itk") pyBasePython
 
 %include <exception.i>
 %include <typemaps.i>
@@ -115,45 +115,8 @@ str = str
                 };
         }
 
-  // some changes in the New() method
-  %rename(__New_orig__) class_name::New;
-  %extend class_name {
-    %pythoncode %{
-      def New(*args, **kargs):
-          """New() -> class_name
-
-          Create a new object of the class class_name and set the input and the parameters if some
-          named or non-named arguments are passed to that method.
-
-          New() tries to assign all the non named parameters to the input of the new objects - the
-          first non named parameter in the first input, etc.
-
-          The named parameters are used by calling the method with the same name prefixed by 'Set'.
-
-          Ex:
-
-            class_name.New( reader, Threshold=10 )
-
-          is (most of the time) equivalent to:
-
-            obj = class_name.New()
-            obj.SetInput( 0, reader.GetOutput() )
-            obj.SetThreshold( 10 )
-          """
-          obj = class_name.__New_orig__()
-          import itkTemplate
-          itkTemplate.New(obj, *args, **kargs)
-          return obj
-      New = staticmethod(New)
-    %}
-  }
-  %pythoncode %{
-    def class_name##_New():
-      return class_name.New()
-  %}
 %enddef
 
-
 %extend itkMetaDataDictionary {
     %ignore Find;
     std::string __str__() {

diff --git a/Wrapping/Generators/Python/Tests/PythonTypeTest.py b/Wrapping/Generators/Python/Tests/PythonTypeTest.py
@@ -65,9 +65,9 @@ def create_and_test(t, create_method):
                 msg = "%s: wrong Python class name: %s" % (actual_type, obj_type)
                 wrongType = 1
         except Exception as e:
-            msg = ("%s: wrong Python class name: %s. "
+            msg = ("%s, %s: wrong Python class name: %s. "
             "Exception while evaluating it: %s" %
-            (t, obj_type, e.message))
+            (t, actual_type, obj_type, e))
             wrongType = 1
     if wrongType:
         print(msg, file=sys.stderr)
@@ -82,7 +82,7 @@ def create_method(i):
         return None
 
 for t in dir(itk):
-    if t not in exclude:
+    if t not in exclude and not t.startswith('stdnumeric_limits'):
         T = itk.__dict__[t]
         # first case - that's a templated class
         if isinstance(T, itk.Vector.__class__) and len(T) > 0:

diff --git a/Wrapping/Generators/Python/Tests/getNameOfClass.py b/Wrapping/Generators/Python/Tests/getNameOfClass.py
@@ -66,15 +66,18 @@ def wrongClassName(cl, name):
             if 'New' in dir(i) and 'GetNameOfClass' in dir(i):
                 totalName += 1
                 if wrongClassName(i, t):
-                    msg = "%s: wrong class name: %s" % (t, n)
+                    msg = "%s: wrong class name: %s" % (T, t)
                     print(msg, file=sys.stderr)
                     wrongName += 1
         else:
             if 'New' in dir(T) and 'GetNameOfClass' in dir(T):
                 totalName += 1
                 if wrongClassName(T, t):
-                    msg = "%s: wrong class name: %s" % (t, n)
+                    msg = "%s: wrong class name: %s" % (T, t)
                     print(msg, file=sys.stderr)
+                    o = T.New()
+                    print(itk.class_(o), file=sys.stderr)
+                    print(o.GetNameOfClass(), file=sys.stderr)
                     wrongName += 1
 
 print("%s classes checked." % totalName)