Merge pull request #5 from nasa/staging/v4.2

Release v4.2

.github/workflows/build-wheels.yml

@@ -1,4 +1,4 @@
-name: Build
+name: Build 🐍 📦 + Publish to PyPI
 
 on:
   push:
@@ -92,9 +92,11 @@ jobs:
             -DUPSP_BUILD_TESTING=OFF -DUPSP_BUILD_APPLICATIONS=OFF -DUPSP_BUILD_PYBIND11=ON'
           CIBW_BEFORE_ALL_LINUX: "yum install -y perl-IPC-Cmd zip ninja-build"
           CIBW_BEFORE_BUILD_WINDOWS: "pip install cmake"
-          CIBW_BUILD: "cp39-win_amd64 cp39-macosx_x86_64 cp39-manylinux_x86_64"
+          CIBW_BUILD: "cp*-win_amd64 cp*-macosx_x86_64 cp*-manylinux_x86_64"
           CIBW_SKIP: "*-win32 *-manylinux_i686"
           CIBW_BUILD_VERBOSITY: 1
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_COMMAND: "pytest {project}/test/python"
         with:
           package-dir: .
           output-dir: wheelhouse
@@ -118,3 +120,24 @@ jobs:
     - uses: actions/upload-artifact@v3
       with:
         path: dist/*.tar.gz
+
+  pypi_publish:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    # Upload for any push of tag starting with 'v'
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          # unpacks default artifact into dist/
+          # if `name: artifact` is omitted, the action will create extra parent dir
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        # For testing
+        # with:
+        #   repository_url: https://test.pypi.org/legacy/

.github/workflows/unit-tests.yml

@@ -1,5 +1,4 @@
-# Run the uPSP project build system and unit tests.
-# Artifacts are installed into the runner's system Python 3 environment.
+# Run the uPSP C++ build system and unit tests.
 #
 # Notes:
 #
@@ -26,10 +25,9 @@
 # - On NAS HECC systems, we build the C/C++ code with dynamic linkage due
 #   to the available system dependencies. This is *not* a default
 #   target supported by vcpkg, but it has a lot of community interest and
-#   "unofficial" testing support. Ref: https://github.com/microsoft/vcpkg/issues/15006
-#   We patch up some of the RPATH quirks using 'patchelf'.
+#   "unofficial" testing support.
 #   
-name: unit-tests
+name: C/C++ unit tests
 on: 
   push: 
   workflow_dispatch:
@@ -51,6 +49,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
       - uses: lukka/get-cmake@latest
       - name: Install dependencies (Linux)
         run: |
@@ -82,33 +82,22 @@ jobs:
           runVcpkgInstall: true
           # Release 2023.04.15
           vcpkgGitCommitId: '501db0f17ef6df184fcdbfbe0f87cde2313b6ab1'
-      - name: Patch vcpkg library headers with patchelf
-        run: |
-          cd vcpkg
-          ${{ github.workspace }}/.github/workflows/vcpkg-fix-rpaths
-          cd ..
-      - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-      - name: Upgrade pip to v23+
-        run: |
-          pip install --upgrade pip
-          pip --version
-          python --version
-      - name: Run build+install with pip
+      - name: Run CMake build
         run: |
-          SKBUILD_CONFIGURE_OPTIONS=\
-          " -DCMAKE_TOOLCHAIN_FILE=${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake"\
-          " -DVCPKG_TARGET_TRIPLET=x64-linux-dynamic" pip install -v .
+          mkdir build
+          cd build
+          cmake \
+            -DCMAKE_TOOLCHAIN_FILE="${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake" \
+            -DVCPKG_TARGET_TRIPLET="x64-linux-dynamic" \
+            -DUPSP_BUILD_TESTING=ON \
+            -DUPSP_BUILD_APPLICATIONS=ON \
+            -DUPSP_BUILD_PYBIND11=ON \
+            ..
+          make -j
       # - name: Setup upterm session
       #   uses: lhotari/action-upterm@v1
       - name: Run C/C++ unit tests
-        # TODO this should be made cross-platform. Currently works only for ubuntu-latest
-        # TODO fix RUNPATH of built executables to avoid use of LD_LIBRARY_PATH
         run: |
-          export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${{ env.VCPKG_INSTALLED_DIR }}/${{ env.VCPKG_DEFAULT_TRIPLET }}/lib"
-          echo "LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
           cd cpp/test
-          ../../_skbuild/linux-x86_64-3.9/cmake-build/run_tests
+          ../../build/cpp/test/run_tests
 

.github/workflows/vcpkg.json

@@ -15,8 +15,5 @@
     "ilmbase",
     "gtest",
     "pybind11"
-  ],
-  "vcpkg-configuration": {
-    "overlay-triplets": ["./vcpkg-triplets"]
-  }
+  ]
 }

cpp/CMakeLists.txt

@@ -1,8 +1,8 @@
 include_directories(include)
 
-option(UPSP_BUILD_APPLICATIONS "Build applications" ON)
-option(UPSP_BUILD_PYBIND11 "Build Python bindings" ON)
-option(UPSP_BUILD_TESTING "Build unit tests" ON)
+option(UPSP_BUILD_APPLICATIONS "Build applications" OFF)
+option(UPSP_BUILD_PYBIND11 "Build Python bindings" OFF)
+option(UPSP_BUILD_TESTING "Build unit tests" OFF)
 
 if (UPSP_BUILD_APPLICATIONS)
     add_subdirectory(exec)

cpp/exec/CMakeLists.txt

@@ -26,7 +26,6 @@ target_link_libraries(upsp-extract-frames opencv_videoio)
 target_include_directories(upsp-extract-frames SYSTEM PRIVATE ${Boost_INCLUDE_DIR})
 
 add_executable(add_field add_field.cpp)
-target_link_libraries(add_field upsp_video)
 target_link_libraries(add_field upsp_utils)
 target_link_libraries(add_field hdf5::hdf5_cpp-shared hdf5::hdf5_hl_cpp-shared)
 

cpp/exec/psp_process.cpp

@@ -1661,7 +1661,21 @@ int phase1(Phase1Settings& sett, P1Elems& elems) {
       // register the image to the first frame
       if (ifile.registration == upsp::RegistrationType::Pixel) {
         cv::Mat warp_matrix;
-        img = upsp::register_pixel(first_frames_32f[c], img, warp_matrix);
+        const int max_iters = 50;
+        const double epsilon = 0.001;
+        int interpolation_flags = 0;
+        switch(ifile.pixel_interpolation) {
+          case upsp::PixelInterpolationType::Linear:
+            interpolation_flags = cv::INTER_LINEAR;
+            break;
+          case upsp::PixelInterpolationType::Nearest:
+            interpolation_flags = cv::INTER_NEAREST;
+            break;
+        }
+        img = upsp::register_pixel(
+          first_frames_32f[c], img, warp_matrix,
+          max_iters, epsilon, interpolation_flags
+        );
       }
 
       // patch frame
@@ -1762,7 +1776,21 @@ int phase1(Phase1Settings& sett, P1Elems& elems) {
         // register the image to the first frame
         if ((f > 0) && (ifile.registration == upsp::RegistrationType::Pixel)) {
           cv::Mat warp_matrix;
-          img = upsp::register_pixel(elems.first_frames[c], img, warp_matrix);
+          const int max_iters = 50;
+          const double epsilon = 0.001;
+          int interpolation_flags = 0;
+          switch(ifile.pixel_interpolation) {
+            case upsp::PixelInterpolationType::Linear:
+              interpolation_flags = cv::INTER_LINEAR;
+              break;
+            case upsp::PixelInterpolationType::Nearest:
+              interpolation_flags = cv::INTER_NEAREST;
+              break;
+          }
+          img = upsp::register_pixel(
+            elems.first_frames[c], img, warp_matrix,
+            max_iters, epsilon, interpolation_flags
+          );
         }
 
         // patch frame

cpp/include/registration.h

@@ -53,13 +53,16 @@ struct RegisterImage : std::unary_function<cv::Mat, cv::Mat> {
  * @param[in] max_iters maximum number of iterations for ECC algorithm
  * @param[in] epsilon   threshold of the increment in correlation coefficient between
  *                      two iterations, criteria for ECC algorithm to stop
+ * @param[in] interpolation_flags pixel interpolation method for image warping
+ *                      two iterations, criteria for ECC algorithm to stop
  * @return              @a inp_img warped to align with @a ref_img
  *
  * @pre @a ref_img and @a inp_img are grayscale images
  * @pre @a ref_img is CV_32F
  */
 cv::Mat register_pixel(const cv::Mat& ref_img, const cv::Mat& inp_img, 
-        cv::Mat& warp_matrix, int max_iters=50, double epsilon=0.001);
+        cv::Mat& warp_matrix, int max_iters=50, double epsilon=0.001,
+        int interpolation_flags=cv::INTER_LINEAR);
 
 /** Remove match pairs where the distance between the points is significantly large
  *

cpp/include/upsp_inputs.h

@@ -26,6 +26,7 @@ enum class TargetPatchType { None, Polynomial };
 
 /** Registration method */
 enum class RegistrationType { None, Point, Pixel };
+enum class PixelInterpolationType { Linear, Nearest };
 
 /** Type of spatial filter */
 enum class FilterType { None, Gaussian, Box };
@@ -78,6 +79,7 @@ class FileInputs {
     GridType grid_type;
     TargetPatchType target_patcher;
     RegistrationType registration;
+    PixelInterpolationType pixel_interpolation;
     FilterType filter;
     OverlapType overlap;
     unsigned int filter_size;
@@ -174,6 +176,9 @@ std::ostream& operator<<(std::ostream& os, const upsp::TargetPatchType& tpt);
 /** Add registration type string to stream */
 std::ostream& operator<<(std::ostream& os, const upsp::RegistrationType& rt);
 
+/** Add pixel interpolation type string to stream */
+std::ostream& operator<<(std::ostream& os, const upsp::PixelInterpolationType& pt);
+
 /** Add filter type string to stream */
 std::ostream& operator<<(std::ostream& os, const upsp::FilterType& ft);
 

cpp/lib/P3DModel.ipp

@@ -5,6 +5,7 @@
  */
 #include "logging.h"
 #include "plot3d.h"
+#include "utils/pspError.h"
 
 namespace upsp {
 

cpp/lib/registration.cpp

@@ -30,7 +30,8 @@ cv::Mat RegisterImage::operator()(cv::Mat inp) {
 
 /*****************************************************************************/
 cv::Mat register_pixel(const cv::Mat& ref_img, const cv::Mat& inp_img, 
-        cv::Mat& warp_matrix, int max_iters/*=50*/, double epsilon/*=0.001*/) {
+        cv::Mat& warp_matrix, int max_iters/*=50*/, double epsilon/*=0.001*/,
+        int interpolation_flags/*=cv::INTER_LINEAR*/) {
 
     // grayscale and ref CV_32F
     assert(ref_img.channels() == 1);
@@ -65,11 +66,15 @@ cv::Mat register_pixel(const cv::Mat& ref_img, const cv::Mat& inp_img,
     // get the warped image
     cv::Mat warp_img;
     if (warp_mode != cv::MOTION_HOMOGRAPHY) {
-        cv::warpAffine(inp_img, warp_img, warp_matrix, ref_img.size(), cv::INTER_LINEAR + 
-                cv::WARP_INVERSE_MAP);
+        cv::warpAffine(
+            inp_img, warp_img, warp_matrix, ref_img.size(),
+            interpolation_flags | cv::WARP_INVERSE_MAP
+        );
     } else {
-        cv::warpPerspective(inp_img, warp_img, warp_matrix, ref_img.size(), cv::INTER_LINEAR + 
-                cv::WARP_INVERSE_MAP);
+        cv::warpPerspective(
+            inp_img, warp_img, warp_matrix, ref_img.size(),
+            interpolation_flags | cv::WARP_INVERSE_MAP
+        );
     }
 
     return warp_img;