Merge branch 'master' into regressionv2

.github/workflows/build-linux-debug.yml

@@ -28,12 +28,6 @@ jobs:
 
     steps:
 
-    - name: Install SSH Key
-      uses: shimataro/[email protected]
-      with:
-        key: ${{ secrets.SSH_PRIVATE_KEY }}
-        known_hosts: ${{ secrets.KNOWN_HOSTS }}
-
     - name: Conda info
       run: conda info
 
@@ -60,10 +54,6 @@ jobs:
     - name: Get tags
       run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
 
-    - name: Restore Caches
-      shell: bash -l {0}
-      run: .github/workflows/restore_caches.sh
-
     - name: Check space3
       run: df -h
 
@@ -83,7 +73,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
 
     - name: Check space6
       run: df -h
@@ -106,9 +96,4 @@ jobs:
     - name: make test
       shell: bash -l {0}
       run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
-
-    - name: Store ccache
-      shell: bash -l {0}
-      run: .github/workflows/store_ccache.sh
-
 

.github/workflows/build-linux.yml

@@ -29,12 +29,6 @@ jobs:
 
     steps:
 
-    - name: Install SSH Key
-      uses: shimataro/[email protected]
-      with:
-        key: ${{ secrets.SSH_PRIVATE_KEY }}
-        known_hosts: ${{ secrets.KNOWN_HOSTS }}
-
     - name: Conda info
       run: conda info
 
@@ -61,10 +55,6 @@ jobs:
     - name: Check space3
       run: df -h
 
-    - name: Restore Caches
-      shell: bash -l {0}
-      run: .github/workflows/restore_caches.sh
-
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
@@ -82,7 +72,7 @@ jobs:
 
     - name: cmake
       shell: bash -l {0}
-      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
+      run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.3 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET ..
 
     - name: Check space5
       run: df -h
@@ -115,10 +105,6 @@ jobs:
       shell: bash -l {0}
       run: conda activate shapeworks && source ./devenv.sh ./build/bin && cd build && ctest -VV
 
-    - name: Copy artifact
-      shell: bash -l {0}
-      run: cd  /__w/ShapeWorks/ShapeWorks/artifacts && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-linux *
-
     - uses: actions/upload-artifact@v2
       with:
         name: artifact-${{github.sha}}-linux
@@ -135,9 +121,4 @@ jobs:
         title: "Development Build for Linux"
         files: |
              ${{runner.workspace}}/ShapeWorks/artifacts/*.tar.gz
-
-    - name: Store ccache
-      shell: bash -l {0}
-      run: .github/workflows/store_ccache.sh
-
       

.github/workflows/build-mac-arm64.yml

@@ -28,12 +28,6 @@ jobs:
 
     steps:
 
-    - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
-      with:
-        key: ${{ secrets.SSH_PRIVATE_KEY }}
-        known_hosts: ${{ secrets.KNOWN_HOSTS }}
-
     - name: Setup Miniconda
       uses: conda-incubator/[email protected]
 
@@ -52,10 +46,6 @@ jobs:
     - name: Get tags
       run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
 
-    - name: Restore Caches
-      shell: bash -l {0}
-      run: .github/workflows/restore_caches.sh
-
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
@@ -115,12 +105,4 @@ jobs:
       env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Store ccache
-      shell: bash -l {0}
-      run: .github/workflows/store_ccache.sh
-
-    - name: Copy artifact
-      shell: bash -l {0}
-      run: cd ${{runner.workspace}}/ShapeWorks && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-mac-arm64 artifacts
 

.github/workflows/build-mac.yml

@@ -28,12 +28,6 @@ jobs:
 
     steps:
 
-    - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
-      with:
-        key: ${{ secrets.SSH_PRIVATE_KEY }}
-        known_hosts: ${{ secrets.KNOWN_HOSTS }}
-
     - name: OS Setup
       run: |
         ls /usr/local
@@ -57,10 +51,6 @@ jobs:
     - name: Get tags
       run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
 
-    - name: Restore Caches
-      shell: bash -l {0}
-      run: .github/workflows/restore_caches.sh
-
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
@@ -120,12 +110,3 @@ jobs:
       env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Store ccache
-      shell: bash -l {0}
-      run: .github/workflows/store_ccache.sh
-
-    - name: Copy artifact
-      shell: bash -l {0}
-      run: cd ${{runner.workspace}}/ShapeWorks && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-mac artifacts
-

.github/workflows/build-windows.yml

@@ -39,7 +39,7 @@ jobs:
     - name: Init conda
       shell: bash -l {0}
       run: /c/Miniconda/condabin/conda.bat init --all
-      
+
     # - name: link
     #   shell: bash -l {0}
     #   run: cd /usr/bin && ln -s /c/Miniconda/condabin/conda.bat conda
@@ -65,12 +65,6 @@ jobs:
     #   with:
     #       miniconda-version: 'latest'
 
-    - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
-      with:
-        key: ${{ secrets.SSH_PRIVATE_KEY }}
-        known_hosts: ${{ secrets.KNOWN_HOSTS }}
-
     - name: Checkout code
       uses: actions/checkout@v3
       with:
@@ -79,16 +73,16 @@ jobs:
     - name: Get tags
       run: git fetch --unshallow origin +refs/tags/*:refs/tags/*
 
+    - name: Download test data
+      shell: bash -l {0}
+      run: .github/workflows/download_test_data.sh
+
     - name: Get NSIS
       working-directory: ${{runner.workspace}}
       run: |
         curl -o nsis.zip http://www.sci.utah.edu/~amorris/NSISPortable_3.04.zip
         Expand-Archive -LiteralPath nsis.zip -DestinationPath .
           
-    - name: Restore Caches
-      shell: bash -l {0}
-      run: .github/workflows/restore_caches.sh
-
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
@@ -115,7 +109,7 @@ jobs:
       # Note the current convention is to use the -S and -B options here to specify source 
       # and build directories, but this is only available with CMake 3.13 and higher.  
       # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.2" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.1" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
+      run: conda activate shapeworks && cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="-FS" -DCMAKE_C_FLAGS="-FS" -DCMAKE_CXX_FLAGS_RELEASE="-FS /Zm500 /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_C_FLAGS_RELEASE="-FS /Zi /GL /MD /O2 /Ob3 /DNDEBUG /EHsc" -DCMAKE_SHARED_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_EXE_LINKER_FLAGS_RELEASE="-LTCG /DEBUG" -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DITK_DIR="C:\deps\lib\cmake\ITK-5.3" -DVTK_DIR="C:\deps\lib\cmake\vtk-9.1" -DXLNT_DIR="C:\deps" -DLIBIGL_DIR="C:\deps" -DJKQTCommonSharedLib_DIR="C:/deps/lib/cmake/JKQTCommonSharedLib" -DJKQTMathTextSharedLib_DIR="C:/deps/lib/cmake/JKQTMathTextSharedLib" -DJKQTPlotterSharedLib_DIR="C:/deps/lib/cmake/JKQTPlotterSharedLib" -DOpenVDB_DIR="C:\deps\lib\cmake\OpenVDB" -DGEOMETRYCENTRAL_DIR="C:\deps" -DACVD_DIR="C:\deps" -DBuild_Studio=ON -DGA_MEASUREMENT_ID=$GA_MEASUREMENT_ID -DGA_API_SECRET=$GA_API_SECRET
 
     - name: Build
       working-directory: "C:/build"
@@ -174,8 +168,3 @@ jobs:
         title: "Development Build for Windows"
         files: |
              d:/a/ShapeWorks/ShapeWorks/artifacts/*.exe
-
-    - name: Copy artifact
-      shell: bash -l {0}
-      run: cd /d/a/ShapeWorks/ShapeWorks/artifacts && ${GITHUB_WORKSPACE}/.github/workflows/copy_artifact.sh artifact-${{github.sha}}-windows *
-

.github/workflows/download_test_data.sh

@@ -13,11 +13,16 @@ BASE=`pwd`
 # based on root folder
 cd /
 
+# if platform is windows, install wget
+if [ "$PLATFORM" == "windows" ]; then
+    choco install wget --no-progress
+fi
 
 # Tiny test data downloads
 for run in {1..5}; do
     if [ ! -f /tmp/tiny_test_cache.tar.gz ] ; then
-	scp runner@${CACHE_HOST}:github/tiny_test_cache.tar.gz /tmp || true
+	cd /tmp
+	wget https://www.sci.utah.edu/~shapeworks/doc-resources/zips/tiny_test_cache.tar.gz || true
 	sleep 1
     fi
 done

.github/workflows/gha_conda.sh

@@ -15,12 +15,6 @@ else
     # run install
     source ./install_shapeworks.sh --developer
     conda clean -p -t -y
-
-    echo "Create and store cache"
-    cd /
-    compress_file /tmp/${CONDA_FILE} "${CONDA_PATH}"
-    scp /tmp/${CONDA_FILE} runner@${CACHE_HOST}:github
-    rm /tmp/${CONDA_FILE}
 fi
 
 conda init bash

.github/workflows/gha_deps.sh

@@ -38,10 +38,4 @@ else
 
     ./build_dependencies.sh --build-type=$BUILD_TYPE --num-procs=$NPROCS --clean-after
     rm -rf $BUILD_DIR
-
-    echo "Create and store cache"
-    cd /
-    compress_file ${FILE} "${DEP_PATH}"
-    scp ${FILE} runner@${CACHE_HOST}:github
-    rm ${FILE}
 fi

CMakeLists.txt

@@ -135,7 +135,7 @@ endif()
 find_package (Eigen3 3.3 REQUIRED NO_MODULE)
 
 ### ITK
-FIND_PACKAGE(ITK 5.2.1 REQUIRED)
+FIND_PACKAGE(ITK 5.3.0 REQUIRED)
 IF (ITK_FOUND)
   INCLUDE(${ITK_USE_FILE})
 ELSE()

Examples/Python/ellipsoid_fd.py

@@ -23,7 +23,7 @@ def Run_Pipeline(args):
     We define dataset_name which determines which dataset to download from 
     the portal and the directory to save output from the use case in. 
     """
-    dataset_name = "ellipsoid_fd"
+    dataset_name = "ellipsoid_fd_multiscale"
     output_directory = "Output/ellipsoid_fd/"
     if not os.path.exists(output_directory):
         os.makedirs(output_directory)

Examples/Python/femur_pvalues.py

@@ -3,14 +3,18 @@
 import numpy as np
 import pandas as pd
 import json
+import zipfile
 
 def Run_Pipeline(args):
     output_directory = 'Output/femur_pvalues/'
     if not os.path.exists(output_directory):
         os.makedirs(output_directory)
 
-    dataset_name = 'femur_pvalues'
-    sw.download_dataset(dataset_name, output_directory)
+    # unzip Data/femur_pvalues.zip
+    zip_file = 'Data/femur_pvalues.zip'
+    with zipfile.ZipFile(zip_file, 'r') as zip_ref:
+        zip_ref.extractall("Output/")
+
     swproj_file = f'{output_directory}/femur_pvalues.swproj'
     csvfile = convert_swproj_to_csv(swproj_file)
     data = pd.read_csv(csvfile)

Examples/Python/supershapes_1mode_contour.py

@@ -9,6 +9,8 @@
 import shapeworks as sw
 import subprocess
 import numpy as np
+import zipfile
+
 from ShapeCohortGen.CohortGenerator import Supershapes2DCohortGenerator
 
 def Run_Pipeline(args):
@@ -21,8 +23,12 @@ def Run_Pipeline(args):
     output_directory = "Output/supershapes_1mode_contour/"
     if not os.path.exists(output_directory):
         os.makedirs(output_directory)
+
     # See the generate_supershapes() function in this file for how the data is generated
-    sw.download_dataset(dataset_name, output_directory)
+    zip_file = 'Data/supershapes_1mode_contour.zip'
+    with zipfile.ZipFile(zip_file, 'r') as zip_ref:
+        zip_ref.extractall("Output/")
+#    sw.download_dataset(dataset_name, output_directory)
     dataset_name = "supershapes2D_1mode"
     contour_files = sorted(glob.glob(output_directory + dataset_name + "/contours/*.vtp"))
 

Libs/Analyze/Shape.cpp

@@ -558,8 +558,8 @@ void Shape::load_feature(DisplayMode display_mode, std::string feature) {
             ImageType::Pointer image = reader->GetOutput();
             group.meshes()[d]->apply_feature_map(feature, image);
             apply_feature_to_points(feature, image);
-          } catch (itk::ExceptionObject& excep) {
-            SW_ERROR("Unable to open file: " + filename);
+          } catch (std::exception& ex) {
+            SW_ERROR("Unable to open file \"{}\": {}", filename, ex.what());
           }
         }
       }
@@ -582,7 +582,7 @@ std::shared_ptr<Image> Shape::get_image_volume(std::string image_volume_name) {
         image_volume_ = image;
         image_volume_filename_ = filename;
       } catch (std::exception& ex) {
-        SW_ERROR("Unable to open file: {}", filename);
+        SW_ERROR("Unable to open file \"{}\": {}", filename, ex.what());
       }
     }
 

Libs/Common/CMakeLists.txt

@@ -3,14 +3,12 @@ set(Common_sources
   Shapeworks.cpp
   ShapeworksUtils.cpp
   Region.cpp
-  Exception.cpp
   Logging.cpp
   )
 set(Common_headers
   Shapeworks.h
   ShapeworksUtils.h
   Region.h
-  Exception.h
   Logging.h
   )
 add_library(Common STATIC