Merge pull request #225 from dzenanz/master

.clang-format

@@ -21,7 +21,7 @@ AccessModifierOffset: -2
 AlignAfterOpenBracket: Align
 AlignConsecutiveAssignments: false
 AlignConsecutiveDeclarations: true
-AlignEscapedNewlines: Right
+AlignEscapedNewlines: Left
 AlignOperands:   true
 AlignTrailingComments: true
 # clang 9.0 AllowAllArgumentsOnNextLine: true

.editorconfig

@@ -1,4 +1,4 @@
-# http://EditorConfig.org
+# https://EditorConfig.org
 
 # top-most EditorConfig file
 root = true

.github/workflows/build-test-package.yml

@@ -4,14 +4,13 @@ on: [push,pull_request]
 
 jobs:
   cxx-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@246883ef3828fc00219145aeec9efa67b9889d0b
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@b223658f3ab10680ab2ec3286d070b9601ea6ef1
     with:
       cmake-options: "Module_Montage_BUILD_EXAMPLES:BOOL=ON"
 
   python-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@246883ef3828fc00219145aeec9efa67b9889d0b
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@b223658f3ab10680ab2ec3286d070b9601ea6ef1
     with:
-      manylinux-platforms: '["_2_28-x64","2014-x64"]'
       test-notebooks: true
     secrets:
       pypi_password: ${{ secrets.pypi_password }}

.github/workflows/clang-format-linter.yml

@@ -7,5 +7,6 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+    - uses: actions/checkout@v3
+
     - uses: InsightSoftwareConsortium/ITKClangFormatLinterAction@master

include/itkTileMontage.h

@@ -203,6 +203,24 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject
     return static_cast<TransformOutputType *>(this->GetOutput(this->nDIndexToLinearIndex(position)))->Get();
   }
 
+  /** Reliability of each tile, highest normalized to 1.0. */
+  using TileReliabilities = std::vector<float>;
+
+  /** Tile reliability, from 0.0 (lowest) to 1.0 (highest).
+   * This can be used to judge successfulness of registration to adjacent tiles. */
+  itkGetConstReferenceMacro(TileReliabilities, TileReliabilities);
+  float
+  GetTileReliability(DataObjectPointerArraySizeType linearIndex) const
+  {
+    return m_TileReliabilities[linearIndex];
+  }
+  float
+  GetTileReliability(TileIndexType nDIndex) const
+  {
+    DataObjectPointerArraySizeType linearIndex = nDIndexToLinearIndex(nDIndex);
+    return GetTileReliability(linearIndex);
+  }
+
 protected:
   TileMontage();
   ~TileMontage() override = default;
@@ -241,6 +259,8 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject
   nDIndexToLinearIndex(TileIndexType nDIndex) const;
   TileIndexType
   LinearIndexTonDIndex(DataObjectPointerArraySizeType linearIndex) const;
+  DataObjectPointerArraySizeType
+  ReferenceLinearIndex(DataObjectPointerArraySizeType candidateIndex) const;
 
   /** Register a pair of images with given indices. Handles FFTcaching. */
   void
@@ -301,6 +321,7 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject
   std::vector<OffsetVector>      m_TransformCandidates; // to adjacent tiles
   std::vector<ConfidencesType>   m_CandidateConfidences;
   std::vector<TranslationOffset> m_CurrentAdjustments;
+  std::vector<float>             m_TileReliabilities;
 
   typename PCMOptimizerType::PeakInterpolationMethodEnum m_PeakInterpolationMethod =
     PCMOptimizerType::PeakInterpolationMethodEnum::Parabolic;

include/itkTileMontage.hxx

@@ -114,6 +114,7 @@ TileMontage<TImageType, TCoordinate>::SetMontageSize(SizeType montageSize)
     m_FFTCache.resize(m_LinearMontageSize);
     m_Tiles.resize(m_LinearMontageSize);
     m_CurrentAdjustments.resize(m_LinearMontageSize);
+    m_TileReliabilities.resize(m_LinearMontageSize);
     m_TransformCandidates.resize(ImageDimension * m_LinearMontageSize); // adjacency along each dimension
     m_CandidateConfidences.resize(ImageDimension * m_LinearMontageSize);
     this->Modified();
@@ -230,6 +231,19 @@ TileMontage<TImageType, TCoordinate>::LinearIndexTonDIndex(DataObject::DataObjec
   return ind;
 }
 
+template <typename TImageType, typename TCoordinate>
+auto
+TileMontage<TImageType, TCoordinate>::ReferenceLinearIndex(DataObjectPointerArraySizeType candidateIndex) const
+  -> DataObjectPointerArraySizeType
+{
+  SizeValueType linIndex = candidateIndex % m_LinearMontageSize;
+  TileIndexType currentIndex = this->LinearIndexTonDIndex(linIndex);
+  TileIndexType referenceIndex = currentIndex;
+  unsigned      dim = candidateIndex / m_LinearMontageSize;
+  referenceIndex[dim] = currentIndex[dim] - 1;
+  return this->nDIndexToLinearIndex(referenceIndex);
+}
+
 template <typename TImageType, typename TCoordinate>
 void
 TileMontage<TImageType, TCoordinate>::RegisterPair(TileIndexType fixed, TileIndexType moving)
@@ -421,11 +435,7 @@ TileMontage<TImageType, TCoordinate>::OptimizeTiles()
     if (!m_TransformCandidates[i].empty())
     {
       SizeValueType linIndex = i % m_LinearMontageSize;
-      TileIndexType currentIndex = this->LinearIndexTonDIndex(linIndex);
-      TileIndexType referenceIndex = currentIndex;
-      unsigned      dim = i / m_LinearMontageSize;
-      referenceIndex[dim] = currentIndex[dim] - 1;
-      SizeValueType refLinearIndex = this->nDIndexToLinearIndex(referenceIndex);
+      SizeValueType refLinearIndex = this->ReferenceLinearIndex(i);
 
       // construct equation: -c*refLinearIndex + c*linIndex = c*candidateOffset, c=confidence
       const float & confidence = m_CandidateConfidences[i][0];
@@ -526,6 +536,8 @@ TileMontage<TImageType, TCoordinate>::OptimizeTiles()
       std::cout << "\nresiduals:\n";
     }
 
+    m_TileReliabilities.clear();
+    m_TileReliabilities.resize(m_LinearMontageSize, 0.0); // reset all to zero
     for (SizeValueType i = 0; i < m_NumberOfPairs; i++)
     {
       TCoordinate residual = 0;
@@ -569,6 +581,67 @@ TileMontage<TImageType, TCoordinate>::OptimizeTiles()
         maxCost = cost;
         maxIndex = i;
       }
+
+      // accumulate costs into tile reliabilities
+      SizeValueType linIndex = candidateIndex % m_LinearMontageSize;
+      SizeValueType refLinearIndex = this->ReferenceLinearIndex(candidateIndex);
+      m_TileReliabilities[linIndex] += cost;
+      m_TileReliabilities[refLinearIndex] += cost;
+    }
+    if (this->GetDebug())
+    {
+      std::cout << std::endl;
+    }
+
+    // now convert costs into reliabilities
+    float minReliabilityCost = std::numeric_limits<float>::max();
+    float maxReliabilityCost = 0.0;
+    // first divide by number of registrations
+    for (SizeValueType i = 0; i < m_LinearMontageSize; ++i)
+    {
+      TileIndexType nDIndex = LinearIndexTonDIndex(i);
+      unsigned      regCount = 2 * Dimension; // for tiles in the middle
+      // now reduce this by one for each dimension's edge this finds itself on
+      for (unsigned d = 0; d < Dimension; ++d)
+      {
+        if (nDIndex[d] == 0 || nDIndex[d] == m_MontageSize[d] - 1)
+        {
+          --regCount;
+        }
+      }
+      assert(regCount >= 1); // every tile must have participated in at least on registration
+      m_TileReliabilities[i] /= regCount;
+      if (m_TileReliabilities[i] < minReliabilityCost)
+      {
+        minReliabilityCost = m_TileReliabilities[i];
+      }
+      if (m_TileReliabilities[i] > maxReliabilityCost)
+      {
+        maxReliabilityCost = m_TileReliabilities[i];
+      }
+    }
+    if (this->GetDebug())
+    {
+      std::cout << "Reliabilities:";
+    }
+    // now transform costs into (0.0, 1.0] reliability range
+    for (SizeValueType i = 0; i < m_LinearMontageSize; ++i)
+    {
+      // map minReliabilityCost to 1.0 reliability; map maxReliabilityCost to near zero (min/max)
+      float sourceRange = maxReliabilityCost - minReliabilityCost;
+      float newMin = minReliabilityCost / maxReliabilityCost;
+      float targetRange = 1.0 - newMin;
+      float fraction = (maxReliabilityCost - m_TileReliabilities[i]) / sourceRange;
+      m_TileReliabilities[i] = newMin + fraction * (targetRange);
+      if (this->GetDebug())
+      {
+        if (i % m_MontageSize[0] == 0)
+        {
+          std::cout << '\n';
+        }
+        std::cout << std::fixed << std::setprecision(4);
+        std::cout << " " << std::setw(6) << m_TileReliabilities[i];
+      }
     }
     if (this->GetDebug())
     {

pyproject.toml

@@ -0,0 +1,112 @@
+[build-system]
+requires = ["scikit-build-core"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "itk-montage"
+version = "0.8.2"
+description = "Montaging for microscopy imaging files."
+readme = "README.md"
+license = {file = "LICENSE"}
+authors = [
+    { name = "Dženan Zukić", email = "[email protected]" },
+    { name = "Matt McCormick", email = "[email protected]" },
+]
+keywords = [
+    "itk",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: Android",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Topic :: Software Development :: Libraries",
+]
+requires-python = ">=3.8"
+dependencies = [
+    "itk-core>=5.4rc4",
+    "itk-filtering>=5.4rc4",
+    "itk-io>=5.4rc4",
+    "numpy",
+]
+
+[project.urls]
+Download = "https://github.com/InsightSoftwareConsortium/ITKMontage"
+Homepage = "https://github.com/InsightSoftwareConsortium/ITKMontage"
+
+[tool.scikit-build]
+# The versions of CMake to allow. If CMake is not present on the system or does
+# not pass this specifier, it will be downloaded via PyPI if possible. An empty
+# string will disable this check.
+cmake.version = ">=3.16.3"
+
+# A list of args to pass to CMake when configuring the project. Setting this in
+# config or envvar will override toml. See also ``cmake.define``.
+cmake.args = []
+
+# A table of defines to pass to CMake when configuring the project. Additive.
+cmake.define = {}
+
+# Verbose printout when building.
+cmake.verbose = true
+
+# The build type to use when building the project. Valid options are: "Debug",
+# "Release", "RelWithDebInfo", "MinSizeRel", "", etc.
+cmake.build-type = "Release"
+
+# The source directory to use when building the project. Currently only affects
+# the native builder (not the setuptools plugin).
+cmake.source-dir = "."
+
+# The versions of Ninja to allow. If Ninja is not present on the system or does
+# not pass this specifier, it will be downloaded via PyPI if possible. An empty
+# string will disable this check.
+ninja.version = ">=1.11"
+
+# The logging level to display, "DEBUG", "INFO", "WARNING", and "ERROR" are
+# possible options.
+logging.level = "INFO"
+
+# Files to include in the SDist even if they are skipped by default. Supports
+# gitignore syntax.
+sdist.include = []
+
+# Files to exclude from the SDist even if they are included by default. Supports
+# gitignore syntax.
+sdist.exclude = []
+
+# A list of license files to include in the wheel. Supports glob patterns.
+wheel.license-files = ["LICEN[CS]E*",]
+
+# Target the platlib or the purelib. If not set, the default is to target the
+# platlib if wheel.cmake is true, and the purelib otherwise.
+wheel.platlib = "false"
+
+# If CMake is less than this value, backport a copy of FindPython. Set to 0
+# disable this, or the empty string.
+backport.find-python = "3.26.1"
+
+# Select the editable mode to use. Can be "redirect" (default) or "inplace".
+editable.mode = "redirect"
+
+# Rebuild the project when the package is imported. The build-directory must be
+# set.
+editable.rebuild = false
+
+# If set, this will provide a method for scikit-build-core backward compatibility.
+minimum-version = "0.8.2"
+
+# The build directory. Defaults to a temporary directory, but can be set.
+build-dir = "build/{wheel_tag}"