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Merge pull request InsightSoftwareConsortium#6103 from hjmjohnson/ingest-Montage
ENH: Ingest ITKMontage remote module into Modules/Registration/Montage Previously passed all tests, only updated to test the behavior of "Populate ExternalData Cache".
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‎Modules/Registration/Montage/CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.16.3)
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if(CMAKE_CXX_STANDARD EQUAL "98")
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message(
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FATAL_ERROR
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"CMAKE_CXX_STANDARD:STRING=98 is not supported in ITK version 5 and greater."
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)
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endif()
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if(NOT CMAKE_CXX_STANDARD)
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set(CMAKE_CXX_STANDARD 17) # Supported values are ``17``, ``20``, and ``23``.
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endif()
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if(NOT CMAKE_CXX_STANDARD_REQUIRED)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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endif()
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if(NOT CMAKE_CXX_EXTENSIONS)
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set(CMAKE_CXX_EXTENSIONS OFF)
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endif()
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project(Montage)
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set(Montage_LIBRARIES Montage)
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# Suppress warnings about potentially uninstantiated static members
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if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
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include(CheckCXXCompilerFlag)
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check_cxx_compiler_flag(
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"-Wno-undefined-var-template"
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COMPILER_HAS_NO_UNDEFINED_VAR_TEMPLATE
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)
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if(COMPILER_HAS_NO_UNDEFINED_VAR_TEMPLATE)
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set(CMAKE_CXX_FLAGS "-Wno-undefined-var-template ${CMAKE_CXX_FLAGS}")
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endif()
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endif()
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if(NOT ITK_SOURCE_DIR)
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find_package(ITK REQUIRED)
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list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
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include(ITKModuleExternal)
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else()
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set(ITK_DIR ${CMAKE_BINARY_DIR})
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itk_module_impl()
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endif()
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itk_module_examples()

‎Modules/Registration/Montage/README.md‎

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# Montage
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Mosaic-stitching and 3D reconstruction of large datasets from a
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collection of partially-overlapping 2D slices, built around phase
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correlation image registration. Core classes:
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- `itk::PhaseCorrelationImageRegistrationMethod`
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- `itk::PhaseCorrelationOperator`
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- `itk::PhaseCorrelationOptimizer`
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- `itk::TileMontage`
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- `itk::TileMergeImageFilter`
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- `itk::TileConfiguration`
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- `itk::NMinimaMaximaImageCalculator`
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## Upstream
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This module was originally developed and maintained as a standalone
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remote module at
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<https://github.com/InsightSoftwareConsortium/ITKMontage>. The
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contents of `include/`, `src/`, `test/`, `wrapping/`, and the two
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CMake build descriptors (`CMakeLists.txt`, `itk-module.cmake`) were
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ingested into ITK via `Utilities/Maintenance/RemoteModuleIngest/`
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(see PR #6098 for the tooling).
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The standalone upstream repository should be treated as archived
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once this ingest lands. Refer to its tags and release history for
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provenance, but future development happens in-tree here.
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## What is intentionally NOT ingested
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The whitelist-based ingest deliberately excludes the following
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upstream content from ITK:
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- `examples/` — applied demonstration code and sample datasets;
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lives with the archived upstream (and selectively relocated to
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[`Examples/`](https://github.com/InsightSoftwareConsortium/ITK/tree/main/Examples)
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in a follow-up PR if broadly useful).
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- `.github/workflows/` — upstream-specific CI configuration; ITK's
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in-tree CI covers the module via the central pipeline.
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- `CTestConfig.cmake` — pointed at a standalone CDash project that
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no longer applies in-tree.
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- `README.md`, `LICENSE`, `requirements.txt`, `pyproject.toml` and
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similar scaffolding — top-level packaging files that are either
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inherited from ITK's own policy (Apache 2.0 license, etc.) or
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irrelevant in-tree.
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If you need any of the above, consult the archived upstream.
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## Compliance level
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Previously tracked as a level-3 remote module (see the superseded
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`Modules/Remote/Montage.remote.cmake`). In-tree placement does not
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automatically raise the compliance level; continued stewardship is
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needed to reach levels 4 and 5.
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## Contact
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Originally authored and maintained by Dženan Zukić
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&lt;dzenan.zukic@kitware.com&gt;. In-tree maintenance follows ITK's
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standard review process.

‎Modules/Registration/Montage/include/itkNMinimaMaximaImageCalculator.h‎

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* https://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#ifndef itkNMinimaMaximaImageCalculator_h
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#define itkNMinimaMaximaImageCalculator_h
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#include "itkMacro.h"
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#include "itkObject.h"
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#include "itkObjectFactory.h"
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#include <mutex>
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#include <vector>
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namespace itk
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{
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/** \class NMinimaMaximaImageCalculator
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* \brief Computes the N highest and/or lowest intensity values of an image.
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*
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* This class is templated over input image type. If only Maxima or
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* Minima are needed, just call ComputeMaxima() or ComputeMinima().
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* Compute() will compute both.
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*
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* \ingroup Operators
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* \ingroup ITKCommon
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* \ingroup Montage
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*/
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template <typename TInputImage>
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class ITK_TEMPLATE_EXPORT NMinimaMaximaImageCalculator : public Object
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{
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public:
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ITK_DISALLOW_COPY_AND_MOVE(NMinimaMaximaImageCalculator);
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/** Standard class type aliases. */
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using Self = NMinimaMaximaImageCalculator;
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using Superclass = Object;
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using Pointer = SmartPointer<Self>;
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using ConstPointer = SmartPointer<const Self>;
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/** Method for creation through the object factory. */
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itkNewMacro(Self);
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/** Run-time type information (and related methods). */
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itkOverrideGetNameOfClassMacro(NMinimaMaximaImageCalculator);
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/** Type definition for the input image. */
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using ImageType = TInputImage;
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/** Pointer type for the image. */
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using ImagePointer = typename TInputImage::Pointer;
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/** Const Pointer type for the image. */
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using ImageConstPointer = typename TInputImage::ConstPointer;
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/** Type definition for the input image pixel type. */
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using PixelType = typename TInputImage::PixelType;
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/** Image dimensionality */
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static constexpr unsigned int ImageDimension = TInputImage::ImageDimension;
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// constexpr unsigned ImageDimension = TInputImage::VImageDimension;
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/** Type definition for the input image index type. */
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using IndexType = typename TInputImage::IndexType;
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/** Type definition for the input image region type. */
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using RegionType = typename TInputImage::RegionType;
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/** Sorted vector of minima or maxima. */
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using ValueVector = std::vector<PixelType>;
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/** Sorted vector of pixel indices of minima or maxima. */
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using IndexVector = std::vector<IndexType>;
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/** Set the input image. */
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itkSetConstObjectMacro(Image, ImageType);
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/** Compute the minimum value of intensity of the input image. */
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void
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ComputeMinima();
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/** Compute the maximum value of intensity of the input image. */
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void
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ComputeMaxima();
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/** Compute the minimum and maximum values of intensity of the input image. */
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void
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Compute();
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/** Return the N minimum intensity values. */
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itkGetConstReferenceMacro(Minima, ValueVector);
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/** Return the N maximum intensity values. */
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itkGetConstReferenceMacro(Maxima, ValueVector);
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/** Return the indices of the N minimum intensity values. */
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itkGetConstReferenceMacro(IndicesOfMinima, IndexVector);
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/** Return the indices of the N maximum intensity values. */
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itkGetConstReferenceMacro(IndicesOfMaxima, IndexVector);
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/** Set the region over which the values will be computed */
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void
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SetRegion(const RegionType & region);
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/** Get/Set the number of extreme intensity values to keep. */
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itkGetConstMacro(N, SizeValueType);
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itkSetMacro(N, SizeValueType);
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protected:
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NMinimaMaximaImageCalculator();
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~NMinimaMaximaImageCalculator() override = default;
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void
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PrintSelf(std::ostream & os, Indent indent) const override;
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template <typename TComparator = std::less<PixelType>>
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void
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SortedInsert(ValueVector & vals,
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IndexVector & indices,
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const PixelType & val,
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const IndexType & ind,
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TComparator comp = TComparator());
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void
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InternalCompute();
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private:
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ImageConstPointer m_Image;
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ValueVector m_Minima;
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ValueVector m_Maxima;
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IndexVector m_IndicesOfMinima;
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IndexVector m_IndicesOfMaxima;
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SizeValueType m_N{ 7 };
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RegionType m_Region;
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bool m_RegionSetByUser{ false };
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bool m_ComputeMaxima{ true };
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bool m_ComputeMinima{ true };
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std::mutex m_Mutex;
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};
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} // end namespace itk
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#ifndef ITK_MANUAL_INSTANTIATION
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# include "itkNMinimaMaximaImageCalculator.hxx"
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#endif
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#endif /* itkNMinimaMaximaImageCalculator_h */

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