[Python-builds] Cleanup python test

Documentation/Maintenance/Release.md

@@ -327,6 +327,22 @@ Add any new remote modules to nightly builds. Some builds may be difficult to ad
 due to third-party dependencies.
 
 
+Update Remote Modules
+---------------------
+
+In order to have the latest versions for all remote modules, and have them use
+the latest ITK tag, the following steps should be performed:
+
+1. Update the ITK tag used in the `azure-pipelines.yml` CI configuration and the
+`setup.py` Python setup files using the [](https://github.com/InsightSoftwareConsortium/ITK/tree/master/Utilities/Maintenance/)
+script. This will involve merging a new pull request to each remote module
+repository.
+
+2. Update the remote modules to their latest commits using the
+[UpdateRemoteModules.sh](https://github.com/InsightSoftwareConsortium/ITK/tree/master/Utilities/Maintenance/UpdateRemoteModules.sh)
+script.
+
+
 Create Tarballs
 ---------------
 

Modules/Filtering/MathematicalMorphology/test/CMakeLists.txt

@@ -524,6 +524,18 @@ itk_add_test(NAME itkRankImageFilterTest10
 # some tests will fail if dim=2 and unsigned short are not wrapped
 list(FIND ITK_WRAP_IMAGE_DIMS 2 wrap_2_index)
 if(ITK_WRAP_unsigned_char AND wrap_2_index GREATER -1)
+  itk_python_add_test(NAME PythonFlatStructuringElementBall
+    TEST_DRIVER_ARGS
+    COMMAND FlatStructuringElementTest.py
+      Ball
+      5
+    )
+  itk_python_add_test(NAME PythonFlatStructuringElementBox
+    TEST_DRIVER_ARGS
+    COMMAND FlatStructuringElementTest.py
+      Box
+      5
+    )
   itk_python_add_test(NAME PythonGrayscaleDilateImageFilterTest
     TEST_DRIVER_ARGS
       --compare ${ITK_TEST_OUTPUT_DIR}/PythonGrayscaleDilateImageFilterTest.png

Wrapping/Generators/Python/Tests/notYetUsable/ImageToArray.py → Modules/Filtering/MathematicalMorphology/test/FlatStructuringElementTest.py

@@ -16,28 +16,18 @@
 #
 #==========================================================================*/
 
-from InsightToolkit import *
-from numarray import *
-from sys import argv
-
-reader = itkImageFileReaderUC2_New()
-
-connector = itkPyBufferUC2_New()
-
-reader.SetFileName(argv[1])
-
-reader.Update()
-
-print "ready to convert image into array"
-
-buffer = connector.GetArrayFromImage(reader.GetOutput())
-
-writer = itkImageFileWriterUC2_New()
-
-writer.SetFileName(argv[2])
-
-print "ready to convert array into image"
-
-writer.SetInput(connector.GetImageFromArray(buffer))
-
-writer.Update()
+from __future__ import print_function
+
+import itk
+from sys import argv, exit
+itk.auto_progress(2)
+
+if argv[1] == "Ball":
+    print("Ball")
+    strel = itk.FlatStructuringElement[2].Ball(int(argv[2]))
+elif argv[1] == "Box":
+    print("Box")
+    strel = itk.FlatStructuringElement[2].Box(int(argv[2]))
+else:
+    print("invalid arguement: " + argv[1])
+    exit(1)

Modules/IO/ImageBase/include/itkImageFileReader.hxx

@@ -26,6 +26,7 @@
 #include "itkVectorImage.h"
 
 #include "itksys/SystemTools.hxx"
+#include <memory>  // For unique_ptr
 #include <fstream>
 
 namespace itk
@@ -388,87 +389,68 @@ void ImageFileReader< TOutputImage, ConvertPixelTraits >
   itkDebugMacro (<< "Setting imageIO IORegion to: " << m_ActualIORegion);
   m_ImageIO->SetIORegion(m_ActualIORegion);
 
-  char *loadBuffer = nullptr;
   // the size of the buffer is computed based on the actual number of
   // pixels to be read and the actual size of the pixels to be read
   // (as opposed to the sizes of the output)
   size_t sizeOfActualIORegion = m_ActualIORegion.GetNumberOfPixels()
                                 * ( m_ImageIO->GetComponentSize() * m_ImageIO->GetNumberOfComponents() );
 
-  try
+  ImageIOBase::IOComponentType ioType =
+    ImageIOBase
+    ::MapPixelType< typename ConvertPixelTraits::ComponentType >::CType;
+  if ( m_ImageIO->GetComponentType() != ioType
+        || ( m_ImageIO->GetNumberOfComponents() !=
+            ConvertPixelTraits::GetNumberOfComponents() ) )
     {
-    ImageIOBase::IOComponentType ioType =
-      ImageIOBase
-      ::MapPixelType< typename ConvertPixelTraits::ComponentType >::CType;
-    if ( m_ImageIO->GetComponentType() != ioType
-         || ( m_ImageIO->GetNumberOfComponents() !=
-              ConvertPixelTraits::GetNumberOfComponents() ) )
-      {
-      // the pixel types don't match so a type conversion needs to be
-      // performed
-      itkDebugMacro( << "Buffer conversion required from: "
-                     << m_ImageIO->GetComponentTypeAsString(m_ImageIO->GetComponentType())
-                     << " to: "
-                     << m_ImageIO->GetComponentTypeAsString(ioType)
-                     << " ConvertPixelTraits::NumComponents "
-                     << ConvertPixelTraits::GetNumberOfComponents()
-                     << " m_ImageIO->NumComponents "
-                     << m_ImageIO->GetNumberOfComponents() );
-
-      loadBuffer = new char[sizeOfActualIORegion];
-      m_ImageIO->Read( static_cast< void * >( loadBuffer ) );
-
-      // See note below as to why the buffered region is needed and
-      // not actualIOregion
-      this->DoConvertBuffer( static_cast< void * >( loadBuffer ),
-                             output->GetBufferedRegion().GetNumberOfPixels() );
-      }
-    else if ( m_ActualIORegion.GetNumberOfPixels() !=
-              output->GetBufferedRegion().GetNumberOfPixels() )
-      {
-      // NOTE:
-      // for the number of pixels read and the number of pixels
-      // requested to not match, the dimensions of the two regions may
-      // be different, therefore we buffer and copy the pixels
-
-      itkDebugMacro(<< "Buffer required because file dimension is greater then image dimension");
+    // the pixel types don't match so a type conversion needs to be
+    // performed
+    itkDebugMacro( << "Buffer conversion required from: "
+                    << m_ImageIO->GetComponentTypeAsString(m_ImageIO->GetComponentType())
+                    << " to: "
+                    << m_ImageIO->GetComponentTypeAsString(ioType)
+                    << " ConvertPixelTraits::NumComponents "
+                    << ConvertPixelTraits::GetNumberOfComponents()
+                    << " m_ImageIO->NumComponents "
+                    << m_ImageIO->GetNumberOfComponents() );
+
+    const std::unique_ptr<char[]> loadBuffer(new char[sizeOfActualIORegion]);
+    m_ImageIO->Read( static_cast< void * >( loadBuffer.get() ) );
+
+    // See note below as to why the buffered region is needed and
+    // not actualIOregion
+    this->DoConvertBuffer( static_cast< void * >( loadBuffer.get() ),
+                            output->GetBufferedRegion().GetNumberOfPixels() );
+    }
+  else if ( m_ActualIORegion.GetNumberOfPixels() !=
+            output->GetBufferedRegion().GetNumberOfPixels() )
+    {
+    // NOTE:
+    // for the number of pixels read and the number of pixels
+    // requested to not match, the dimensions of the two regions may
+    // be different, therefore we buffer and copy the pixels
 
-      OutputImagePixelType *outputBuffer = output->GetPixelContainer()->GetBufferPointer();
+    itkDebugMacro(<< "Buffer required because file dimension is greater then image dimension");
 
-      loadBuffer = new char[sizeOfActualIORegion];
-      m_ImageIO->Read( static_cast< void * >( loadBuffer ) );
+    OutputImagePixelType *outputBuffer = output->GetPixelContainer()->GetBufferPointer();
 
-      // we use std::copy here as it should be optimized to memcpy for
-      // plain old data, but still is oop
-      std::copy(reinterpret_cast< const OutputImagePixelType * >( loadBuffer ),
-                             reinterpret_cast< const OutputImagePixelType * >( loadBuffer ) + output->GetBufferedRegion().GetNumberOfPixels(),
-                             outputBuffer);
-      }
-    else
-      {
-      itkDebugMacro(<< "No buffer conversion required.");
+    const std::unique_ptr<char[]> loadBuffer(new char[sizeOfActualIORegion]);
+    m_ImageIO->Read( static_cast< void * >( loadBuffer.get() ) );
 
-      OutputImagePixelType *outputBuffer = output->GetPixelContainer()->GetBufferPointer();
-      m_ImageIO->Read(outputBuffer);
-      }
+    // we use std::copy_n here as it should be optimized to memcpy for
+    // plain old data, but still is oop
+    std::copy_n(reinterpret_cast< const OutputImagePixelType * >( loadBuffer.get() ),
+                            output->GetBufferedRegion().GetNumberOfPixels(),
+                            outputBuffer);
     }
-  catch ( ... )
+  else
     {
-    // if an exception is thrown catch it
-
-    // clean up
-    delete[] loadBuffer;
-    loadBuffer = nullptr;
+    itkDebugMacro(<< "No buffer conversion required.");
 
-    // then rethrow
-    throw;
+    OutputImagePixelType *outputBuffer = output->GetPixelContainer()->GetBufferPointer();
+    m_ImageIO->Read(outputBuffer);
     }
 
   this->UpdateProgress( 1.0f );
-
-  // clean up
-  delete[] loadBuffer;
-  loadBuffer = nullptr;
 }
 
 template< typename TOutputImage, typename ConvertPixelTraits >

Utilities/Maintenance/UpdateRemoteModules.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+#==========================================================================
+#
+#   Copyright Insight Software Consortium
+#
+#   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.
+#
+#==========================================================================*/
+
+
+# Make sure we are inside the repository
+cd "${BASH_SOURCE%/*}" &&
+
+remote_modules_path=$(cd ../../Modules/Remote && pwd)
+
+git_repository_tag_label='GIT_REPOSITORY'
+git_tag_label='GIT_TAG'
+
+# Loop over the remote modules' CMake files
+for filename in ${remote_modules_path}/*.cmake; do
+
+  # Get the current commit hash
+  curr_commit_str=($(grep $git_tag_label $filename))
+  curr_commit_hash=${curr_commit_str[1]}
+
+  # Read the git repository information
+  repository_str=$(grep $git_repository_tag_label $filename)
+
+  repository_arr=($(echo $repository_str | tr "/" " "))
+  organization=${repository_arr[-2]}
+  repository_name=${repository_arr[-1]}
+
+  # Get the latest git commit hash of the remote module.
+  # Remotes will usually not be tagged.
+  latest_commit_hash=$(git ls-remote git://github.com/$organization/$repository_name | \
+  grep refs/heads/master | cut -f 1)
+
+  # Sed the the latest commit hash in the CMake file
+  sed -i "s/${curr_commit_hash}/${latest_commit_hash}/g" $filename
+
+done

Utilities/Maintenance/UpdateRequiredITKVersionInFiles.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+
+#==========================================================================
+#
+#   Copyright Insight Software Consortium
+#
+#   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.
+#
+#==========================================================================*/
+
+
+program_name=$0
+
+function usage {
+  echo "Usage: ${program_name} "
+  echo "  param1 Azure pipelines file path"
+  echo "  param2 Setup.py file path"
+  exit 1
+}
+
+# Display usage
+if [ ${#@} != 2 ]; then
+  usage
+fi
+
+azure_pipelines_ci_filename=$1
+python_setup_filename=$2
+
+# Get the latest ITK git tag
+latest_git_tag=$(git ls-remote --tags --sort="v:refname" \
+git://github.com/InsightSoftwareConsortium/ITK.git | tail -n1 | \
+sed 's/.*\///; s/\^{}//')
+
+# Azure pipeline CI file
+git_tag_label='ITKGitTag: '
+
+# Read the ITK git tag information
+curr_git_str=($(grep $git_tag_label $filename))
+curr_git_tag=${curr_git_str[1]}
+
+# Sed the latest ITK git tag in the Azure pipelines config file
+sed -i "s/${curr_git_tag}/${latest_git_tag}/g" $azure_pipelines_ci_filename
+
+# Python setup file
+
+# Strip the "v" prefix
+latest_git_tag=${latest_git_tag:1}
+
+git_install_req_tag_label='\install_requires=\['
+
+# Read the ITK install requirement git tag information
+git_install_req_tag_str=($(grep -A1 -P ${git_install_req_tag_label}$ $filename))
+git_install_req_tag=${git_install_req_tag_str[1]}
+
+git_install_req_tag_arr=($(echo $git_install_req_tag | tr "=" " "))
+curr_git_tag=${git_install_req_tag_arr[-1]}
+
+# Sed the latest ITK git tag in the Python setup file
+sed -i "s/${curr_git_tag}/${latest_git_tag}/g" $python_setup_filename