Merge pull request #15 from NiftyPET/devel

next release: v2.1.0
NiftyPET · Jan 31, 2021 · 4cc642f · 4cc642f
2 parents 847aedd + d9ebb0b
commit 4cc642f
Show file tree

Hide file tree

Showing 20 changed files with 564 additions and 404 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -2,15 +2,14 @@ name: Test
 on: [push, pull_request]
 jobs:
   check:
+    if: github.event_name != 'push' || github.ref != 'refs/heads/devel'
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [3.6, 3.9]
     name: Check py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
     - uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
@@ -25,7 +24,8 @@ jobs:
         pip install -U pre-commit
         sudo apt-get install -yqq clang-format
     - uses: reviewdog/action-setup@v1
-    - name: comment
+    - if: github.event_name != 'schedule'
+      name: comment
       run: |
         if [[ $EVENT == pull_request ]]; then
           REPORTER=github-pr-review
@@ -41,20 +41,21 @@ jobs:
   test:
     if: github.event_name != 'pull_request' || github.head_ref != 'devel'
     runs-on: [self-hosted, cuda, python]
-    name: Test
+    strategy:
+      matrix:
+        python: [3.6, 3.9]
+    name: Test py${{ matrix.python }}
     steps:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
     - name: Run setup-python
-      run: setup-python -p3.7 -m ${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}
+      run: setup-python -p${{ matrix.python }}
     - run: pip install -U -e .[dev]
     - run: pytest
     - run: codecov
-      env:
-        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
     - name: Post Run setup-python
-      run: setup-python -p3.7 -m ${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER} -r
+      run: setup-python -p${{ matrix.python }} -Dr
       if: ${{ always() }}
   deploy:
     needs: [check, test]
@@ -65,30 +66,25 @@ jobs:
       with:
         fetch-depth: 0
     - uses: actions/setup-python@v2
-    - run: pip install -U twine setuptools wheel setuptools_scm[toml] ninst scikit-build
-    - run: PATHTOOLS=$HOME/NiftyPET_tools python setup.py sdist
-    - run: twine check dist/*
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      run: twine upload dist/*
+    - id: dist
+      uses: casperdcl/deploy-pypi@v2
+      with:
+        requirements: twine setuptools wheel setuptools_scm[toml] ninst scikit-build
+        build: sdist
+        password: ${{ secrets.PYPI_TOKEN }}
+        upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }}
       env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
-        skip_existing: true
-    - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      id: collect_assets
-      name: Collect assets
-      run: |
-        echo "::set-output name=asset_path::$(ls dist/*.tar.gz)"
-        echo "::set-output name=asset_name::$(basename dist/*.tar.gz)"
-        git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
+        PATHTOOLS: ${{ github.workspace }}/NiftyPET_tools
+    - name: Changelog
+      run: git log --pretty='format:%d%n- %s%n%b---' $(git tag --sort=v:refname | tail -n2 | head -n1)..HEAD > _CHANGES.md
     - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
       id: create_release
       uses: actions/create-release@v1
       env:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
         tag_name: ${{ github.ref }}
-        release_name: nimpa ${{ github.ref }} beta
+        release_name: nimpa ${{ github.ref }} stable
         body_path: _CHANGES.md
         draft: true
     - if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
@@ -97,6 +93,6 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
       with:
         upload_url: ${{ steps.create_release.outputs.upload_url }}
-        asset_path: ${{ steps.collect_assets.outputs.asset_path }}
-        asset_name: ${{ steps.collect_assets.outputs.asset_name }}
+        asset_path: dist/${{ steps.dist.outputs.targz }}
+        asset_name: ${{ steps.dist.outputs.targz }}
         asset_content_type: application/gzip
diff --git a/.gitignore b/.gitignore
@@ -13,5 +13,5 @@ MANIFEST
 /*.egg*/
 /.eggs/
 
-/.coverage
+/.coverage*
 /coverage.xml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -25,12 +25,6 @@ repos:
     types: [text]
     exclude: ^(.pre-commit-config.yaml|.github/workflows/test.yml)$
     args: [-i]
-- repo: https://github.com/doublify/pre-commit-clang-format
-  rev: master
-  hooks:
-  - id: clang-format
-    files: \.(cc?|cuh?|cxx|cpp|h|hpp|hxx|java|js)$
-    args: ['-fallback-style=none', '-style={BasedOnStyle: LLVM, ColumnLimit: 99}']
 - repo: https://gitlab.com/pycqa/flake8
   rev: 3.8.4
   hooks:
@@ -49,3 +43,9 @@ repos:
   rev: 5.7.0
   hooks:
   - id: isort
+- repo: https://github.com/doublify/pre-commit-clang-format
+  rev: master
+  hooks:
+  - id: clang-format
+    files: \.(cc?|cuh?|cxx|cpp|h|hpp|hxx|java|js)$
+    args: ['-fallback-style=none', '-style={BasedOnStyle: LLVM, ColumnLimit: 99, AllowShortBlocksOnASingleLine: true, AllowShortIfStatementsOnASingleLine: true, AllowShortLoopsOnASingleLine: true}']
diff --git a/.zenodo.json b/.zenodo.json
@@ -0,0 +1,12 @@
+{
+  "title": "NIMPA: High-throughput neuroimage processing and analysis",
+  "keywords": ["PET", "MR", "processing", "analysis", "GPU"],
+  "related_identifiers": [
+    {"identifier": "10.1007/s12021-017-9352-y", "relation": "documents"},
+    {"identifier": "10.1088/0031-9155/61/13/N322", "relation": "documents"}],
+  "creators": [
+    {"name": "Markiewicz, Pawel J.", "orcid": "0000-0002-3114-0773",
+     "affiliation": "University College London"},
+    {"name": "da Costa-Luis, Casper O.", "orcid": "0000-0002-7211-1557",
+     "affiliation": "King's College London, University College London"}]
+}
diff --git a/niftypet/CMakeLists.txt b/niftypet/CMakeLists.txt
@@ -1,25 +1,52 @@
 cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
 if("${NIMPA_BUILD_VERSION}" STREQUAL "")
-set(NIMPA_BUILD_VERSION 2 CACHE STRING "version" FORCE)
+  set(NIMPA_BUILD_VERSION 2 CACHE STRING "version" FORCE)
 endif()
 project(nimpa LANGUAGES C CXX CUDA VERSION "${NIMPA_BUILD_VERSION}")
 
 cmake_policy(PUSH)
 cmake_policy(SET CMP0074 NEW)  # <PackageName>_ROOT hints for find_package
 cmake_policy(SET CMP0104 NEW)  # CMAKE_CUDA_ARCHITECTURES
-find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
+find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
 find_package(CUDAToolkit REQUIRED)
+execute_process(
+  COMMAND "${Python3_EXECUTABLE}" -c "import cuvec; print(cuvec.include_path)"
+  OUTPUT_VARIABLE CUVEC_INCLUDE_DIRS
+  OUTPUT_STRIP_TRAILING_WHITESPACE)
+if("${CUVEC_INCLUDE_DIRS}" STREQUAL "")
+  message(WARNING "Could not find cuvec includes")
+else()
+  message(STATUS "Found cuvec includes: ${CUVEC_INCLUDE_DIRS}")
+endif()
 if(SKBUILD)
-find_package(PythonExtensions REQUIRED)
+  find_package(PythonExtensions REQUIRED)
+  set(LIB_TYPE "MODULE")
+else()
+  set(LIB_TYPE "SHARED")
 endif()
 cmake_policy(POP)
 
 message(STATUS "CUDA architectures: ${CMAKE_CUDA_ARCHITECTURES}")
 if("${CMAKE_BUILD_TYPE}" STREQUAL "")
-set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
 endif()
 message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 
+option(CUVEC_DEBUG "Print out CUDA malloc & free operations" OFF)
+if(CUVEC_DEBUG)
+  add_compile_definitions(CUVEC_DEBUG)
+endif(CUVEC_DEBUG)
+message(STATUS "cuvec debugging: ${CUVEC_DEBUG}")
+if("${NIMPA_CU_THREADS}" STREQUAL "")
+  set(NIMPA_CU_THREADS 1024 CACHE STRING
+    "Maximum number of CUDA threads per block (should be less than cudaDeviceProp::maxThreadsDim)" FORCE)
+endif()
+add_compile_definitions(NIMPA_CU_THREADS=${NIMPA_CU_THREADS})
+if("${NIMPA_KERNEL_RADIUS}" STREQUAL "")
+  set(NIMPA_KERNEL_RADIUS 8 CACHE STRING "Maximum kernel half-width (excluding central voxel)" FORCE)
+endif()
+add_compile_definitions(NIMPA_KERNEL_RADIUS=${NIMPA_KERNEL_RADIUS})
+
 add_subdirectory(nimpa)
 
 include(CMakePackageConfigHelpers)

diff --git a/niftypet/nimpa/include/conv.h b/niftypet/nimpa/include/conv.h
@@ -1,13 +1,21 @@
 #ifndef _NIMPA_CONV_H_
 #define _NIMPA_CONV_H_
 
-// for logging
+// logging levels
 #define LOGDEBUG 10
 #define LOGINFO 20
 #define LOGWARNING 30
 
-#define RSZ_PSF_KRNL 8
-#define KERNEL_LENGTH (2 * RSZ_PSF_KRNL + 1)
+// number of threads used for element-wise GPU calculations
+#ifndef NIMPA_CU_THREADS
+#define NIMPA_CU_THREADS 1024
+#endif
+
+/* separable convolution */
+#ifndef NIMPA_KERNEL_RADIUS
+#define NIMPA_KERNEL_RADIUS 8
+#endif
+#define KERNEL_LENGTH (2 * NIMPA_KERNEL_RADIUS + 1)
 
 // Column convolution filter
 #define COLUMNS_BLOCKDIM_X 8
@@ -26,9 +34,14 @@ struct Cnst {
   char LOG;   // logging
 };
 
-// GPU convolution
-void setConvolutionKernel(float *hKrnl);
+/// krnl: separable three kernels for x, y and z
+void setConvolutionKernel(float *krnl, bool handle_errors = true);
+
+/// sigma: Gaussian sigma
+void setKernelGaussian(float sigma, bool handle_errors = true);
 
-void gpu_cnv(float *imgout, float *imgint, int Nvk, int Nvj, int Nvi, Cnst Cnt);
+/// main convolution function
+void d_conv(float *dst, float *src, int Nvk, int Nvj, int Nvi, bool _memset = true,
+            bool _sync = true);
 
 #endif // _NIMPA_CONV_H_
diff --git a/niftypet/nimpa/include/cuhelpers.h b/niftypet/nimpa/include/cuhelpers.h
@@ -0,0 +1,10 @@
+#ifndef _CU_HELPERS_
+#define _CU_HELPERS_
+
+void HandleError(cudaError_t err, const char *file, int line);
+#define HANDLE_ERROR(err) (HandleError(err, __FILE__, __LINE__))
+
+bool PyHandleError(cudaError_t err, const char *file, int line);
+#define HANDLE_PyErr(err) (PyHandleError(err, __FILE__, __LINE__))
+
+#endif // _CU_HELPERS_
diff --git a/niftypet/nimpa/include/rsmpl.h b/niftypet/nimpa/include/rsmpl.h
@@ -34,6 +34,6 @@ struct Cimg {
   float OFFRz;
 };
 
-float *rsmpl(float *imo, float *A, Cimg Cim);
+void rsmpl(float *imt, float *imo, float *A, Cimg Cim, bool _memset = true, bool _sync = true);
 
 #endif // _NIMPA_RSMPL_H_
diff --git a/niftypet/nimpa/prc/CMakeLists.txt b/niftypet/nimpa/prc/CMakeLists.txt
@@ -1,11 +1,11 @@
 project(improc)
 
-file(GLOB SRC LIST_DIRECTORIES false "src/*.cu" "src/*.h")
-
+file(GLOB SRC LIST_DIRECTORIES false "src/*.cu")
+include_directories(src)
 include_directories(${Python3_INCLUDE_DIRS})
-include_directories(${Python3_NumPy_INCLUDE_DIRS})
+include_directories(${CUVEC_INCLUDE_DIRS})
 
-add_library(${PROJECT_NAME} MODULE ${SRC})
+add_library(${PROJECT_NAME} ${LIB_TYPE} ${SRC})
 add_library(NiftyPET::${PROJECT_NAME} ALIAS ${PROJECT_NAME})
 target_include_directories(${PROJECT_NAME} PUBLIC
   "$<BUILD_INTERFACE:${${CMAKE_PROJECT_NAME}_INCLUDE_DIRS}>"
@@ -14,8 +14,8 @@ target_link_libraries(${PROJECT_NAME} ${Python3_LIBRARIES} ${CUDA_LIBRARIES} ${C
 if(SKBUILD)
 python_extension_module(${PROJECT_NAME})
 endif()
-
 set_target_properties(${PROJECT_NAME} PROPERTIES
+  CXX_STANDARD 11
   VERSION ${CMAKE_PROJECT_VERSION}
   SOVERSION ${CMAKE_PROJECT_VERSION_MAJOR}
   INTERFACE_${PROJECT_NAME}_MAJOR_VERSION ${CMAKE_PROJECT_VERSION_MAJOR})