fix visiblity determination for subtomo particle reconstruction

CMakeLists.txt

@@ -1,8 +1,5 @@
-cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.21 FATAL_ERROR)
 
-#if(POLICY CMP0048)
-#  cmake_policy(SET CMP0048 NEW)
-#endif()
 project(Relion)
 
 # Use new policy for OS X @rpath
@@ -72,13 +69,12 @@ endif()
 
 # ----------------------------------------------------------------SET CXX STANDARD--
 set(CXX_STANDARD_REQUIRED ON)
-if(SYCL)
-	set(CMAKE_CXX_STANDARD 17)
-else()
-	set(CMAKE_CXX_STANDARD 14)
-endif()
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
+set(C_STANDARD_REQUIRED ON)
+set(CMAKE_C_STANDARD 99)
+
 # ------------------OPTIONS WHICH ARE NEEDED TO SET BUILD-TYPES (COMPILATION FLAGS)--
 # -------------------------------------------------------------------FURTHER OPTIONS--
 
@@ -170,48 +166,47 @@ else(DoublePrec_ACC)
 endif(DoublePrec_ACC)
 
 if(MDT_TYPE_CHECK)
-    message("-- MetaDataTable type check is enabled.")
+	message(STATUS "MetaDataTable type check is enabled.")
     add_definitions(-DMETADATA_TABLE_TYPE_CHECK)
 endif()
 
 if(CUDA)
     # -----------------------------------------------------------------------------CUDA--
-    # DOC: http://www.cmake.org/cmake/help/v3.0/module/FindCUDA.html
-    FIND_PACKAGE(CUDA)
-
-    # "-arch=sm_XX" alone is equal to "-arch=compute_XX -code=compute_XX,sm_XX"
-    # compute_XX generates PTX; thus GPUs newer than XX can also use the binary.
-    # See https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/#gpu-architecture-arch.
-    set(CUDA_ARCH "" CACHE STRING "CUDA architecture to use")
-    if (CUDA_ARCH STREQUAL "")
-        if (${CUDA_VERSION} VERSION_LESS "13.0") # Pascal (e.g. 1080)
-            message(STATUS "Setting fallback CUDA_ARCH=50 (Pascal)")
-            set(CUDARCH "-arch=sm_50")
-        else() # CUDA >= 13.0 no longer supports Pascal. 75 = Turing (e.g. 2080) 
-            message(STATUS "Setting fallback CUDA_ARCH=75 (Turing)")
-            set(CUDARCH "-arch=sm_75")
-        endif()
-    else ()
-        message(STATUS "Using provided CUDA_ARCH=${CUDA_ARCH}")
-        set(CUDARCH "-arch=sm_${CUDA_ARCH}")
-    endif ()
-
-    if(CUDA_FOUND)
-      message(STATUS "Using cuda wrapper to compile....")
-      if( (NOT ${CUDA_VERSION} VERSION_LESS "7.5") AND (NOT DoublePrec_ACC) )
-          message(STATUS "Cuda version is >= 7.5 and single-precision build, enable double usage warning.")
-		      set(WARN_DBL "--ptxas-options=-warn-double-usage") # cuda>=7.5
-	    elseif( ${CUDA_VERSION} VERSION_LESS "7.0")
-		      message(WARNING "Cuda version is less than 7.0, so relion will be compiled without GPU support.")
-          message(STATUS "Using non-cuda compilation....")
-		      set(CUDA OFF)
-      endif()
-      if(CUDA)
-          add_definitions(-D_CUDA_ENABLED)
-      endif()
-    else(CUDA_FOUND)
-        message(FATAL_ERROR "CUDA enabled but unlable to locate packages...")
-    endif(CUDA_FOUND)
+    FIND_PACKAGE(CUDAToolkit)
+
+    if((CUDAToolkit_FOUND) AND ("${CUDAToolkit_VERSION}" VERSION_GREATER_EQUAL "10.0"))
+	    message(STATUS "CUDAToolkit discovered CUDA " ${CUDAToolkit_VERSION} " at " ${CUDAToolkit_BIN_DIR})
+        set(CMAKE_CUDA_STANDARD 17)
+
+        # Very puzzling but `CUDAToolkit` package and `enable_language(CUDA)` use
+        # different methods to find `nvcc`. The latter does NOT respect `PATH` (`which nvcc`) and
+        # can pick up /usr/bin/nvcc. We can override this by setting `CMAKE_CUDA_COMPILER`.
+        # Another useful variable is `CMAKE_CUDA_HOST_COMPILER`.
+        set(CMAKE_CUDA_COMPILER "${CUDAToolkit_BIN_DIR}/nvcc" CACHE FILEPATH "Path to the CUDA compiler (nvcc)")
+        enable_language(CUDA)
+
+        # "-arch=sm_XX" alone is equal to "-arch=compute_XX -code=compute_XX,sm_XX"
+        # compute_XX generates PTX; thus GPUs newer than XX can also use the binary.
+        # See https://docs.nvidia.com/cuda/cuda-compiler-driver-nvcc/#gpu-architecture-arch.
+        set(CUDA_ARCH "" CACHE STRING "CUDA architecture to use")
+        if (CUDA_ARCH STREQUAL "")
+            if (${CUDAToolkit_VERSION} VERSION_LESS "13.0") # Pascal (e.g. 1080)
+                message(STATUS "Setting fallback CUDA_ARCH=50 (Pascal)")
+                set(CMAKE_CUDA_ARCHITECTURES 50)
+            else() # CUDA >= 13.0 no longer supports Pascal. 75 = Turing (e.g. 2080)
+                message(STATUS "Setting fallback CUDA_ARCH=75 (Turing)")
+                set(CMAKE_CUDA_ARCHITECTURES 75)
+            endif()
+        else ()
+            message(STATUS "Using provided CUDA_ARCH=${CUDA_ARCH}")
+            set(CMAKE_CUDA_ARCHITECTURES ${CUDA_ARCH})
+        endif ()
+
+        add_definitions(-D_CUDA_ENABLED)
+    else()
+        message("!! CUDA was enabled but CUDA >= 10.0 cannot be located. CUDA is set to OFF.")
+        set(CUDA OFF)
+    endif()
 elseif(HIP)
     # ------------------------------------------------------------------------------HIP--
     if (DEFINED ENV{ROCM_PATH})
@@ -257,6 +252,24 @@ elseif(ALTCPU)
 	endif()
 endif()
 
+# ----------------------------------------------------------------- OpenMP ----------
+# This must come before including BuildTypes.cmake to properly set OpenMP flags to NVCC.
+# CUDA support by the OpenMP package came at CMake 3.31 (too new).
+
+if(SYCL) # Intel DPC++ specific; I don't know when the OpenMP package supports SYCL
+	set(OpenMP_C_FLAGS "-fiopenmp")
+	set(OpenMP_CXX_FLAGS "-fiopenmp")
+	set(OpenMP_EXE_LINKER_FLAGS "-fiopenmp")
+else()
+	FIND_PACKAGE(OpenMP REQUIRED)
+endif()
+
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+set(CMAKE_CXX_FLAGS "-fPIC ${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+
+#message(STATUS "OpenMP_CXX_FLAGS: ${OpenMP_CXX_FLAGS}")
+
 # ----------------------------------------------------------INCLUDE ALL BUILD TYPES---
 # This has to be AFTER project() and find_package(HIP).
 # Up to RELION 5.0.0, this must come BEFORE find_package(CUDA) as discussed in issue #1032.
@@ -372,29 +385,6 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
-# ----------------------------------------------------------------- OpenMP ----------
-# This MUST be set before all cuda_add_executable/library calls.
-# Otherwise the -Xcompiler argument to NVCC does not contain -fopenmp
-# and #pragma omp critical is SILENTLY ignored, giving a wrong binary!!!
-# https://github.com/3dem/relion/issues/1016
-
-if(SYCL)    # Intel DPC++ specific
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fiopenmp")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fiopenmp")
-	set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fiopenmp")
-
-	set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")
-	set(CMAKE_CXX_FLAGS "-fPIC -std=c++17 ${CMAKE_CXX_FLAGS}")
-else()
-	FIND_PACKAGE(OpenMP REQUIRED)
-	set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-	set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
-
-	set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")
-	set(CMAKE_CXX_FLAGS "-fPIC -std=c++17 ${CMAKE_CXX_FLAGS}")
-endif()
-
 # ----------------------------------------------------------Intel Compiler support --
 # ----------------------------------  and build flags including MKL and IPP ---------
 
@@ -486,9 +476,9 @@ if(GUI)
 	endif(NOT FLTK_FOUND)
 
     else(X11_FOUND)
-        message( STATUS "\n-- ------------------ YOU HAVE NO X11-LIBS ------------------")
-        message( STATUS "CCmake found no X11-libs on your system, which are required for the GUI.")
-        message( STATUS " You CAN add the flag -DGUI=OFF to avoid using X11" )
+        message(STATUS "\n-- ------------------ YOU HAVE NO X11-LIBS ------------------")
+        message(STATUS "CCmake found no X11-libs on your system, which are required for the GUI.")
+        message(STATUS " You CAN add the flag -DGUI=OFF to avoid using X11" )
         message(FATAL_ERROR "X11 is required for GUI.")
     endif(X11_FOUND)
 
@@ -551,7 +541,7 @@ endif(JPEG_FOUND)
 # -----------------------------------------------------------------PYTHON DEPENDENCIES--
 
 
-set(CONDA_ENV_NAME "relion-5.0" CACHE STRING "The Conda environment name")
+set(CONDA_ENV_NAME "relion-5.1" CACHE STRING "The Conda environment name")
 include(${CMAKE_SOURCE_DIR}/cmake/FindCondaPython.cmake)
 
 list(APPEND RELION_PYTHON_WRAPPERS
@@ -569,6 +559,8 @@ list(APPEND RELION_PYTHON_WRAPPERS
 	python_tomo_get_particle_poses
 	python_tomo_denoise
 	filament_selection
+	python_trace_amyloids
+	schemegui
 )
 
 foreach (SCRIPT_FILE ${RELION_PYTHON_WRAPPERS})
@@ -587,6 +579,12 @@ if (FETCH_WEIGHTS)
 			"NOTE: You can skip this step by setting -DFETCH_WEIGHTS=OFF"
 	)
 
+	# `relion_trace_amyloids.py` is necessary for weight download during `cmake`.
+	# The `copy_scripts` target below is executed only during `make`.
+	configure_file("${CMAKE_SOURCE_DIR}/scripts/trace_amyloids.py"
+	               "${CMAKE_BINARY_DIR}/bin/relion_trace_amyloids.py"
+	               COPYONLY)
+
 	execute_process(
 			COMMAND bash ${CMAKE_BINARY_DIR}/bin/relion_python_fetch_weights
 			WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
@@ -623,7 +621,7 @@ list(APPEND RELION_SCRIPT_FILES
         star_datablock_ctfdat
         qsub.csh
         it.py
-        schemegui.py
+	trace_amyloids.py
 )
 
 add_custom_target(copy_scripts ALL)
@@ -675,6 +673,11 @@ message(STATUS "CMAKE_CXX_FLAGS : ${CMAKE_CXX_FLAGS}")
 #message(STATUS "MPI_C_COMPILER : ${MPI_C_COMPILER}")
 #message(STATUS "MPI_CXX_COMPILER : ${MPI_CXX_COMPILER}")
 #message(STATUS "CMAKE_EXE_LINKER_FLAGS : ${CMAKE_EXE_LINKER_FLAGS}")
+#message(STATUS "CUDAToolkit_FOUND: ${CUDAToolkit_FOUND}")
+#get_target_property(CUDART_LIB CUDA::cudart IMPORTED_LOCATION)
+#message(STATUS "CUDA::cudart location: ${CUDART_LIB}")
+#get_target_property(CUDART_INC CUDA::cudart INTERFACE_INCLUDE_DIRECTORIES)
+#message(STATUS "CUDA::cudart includes: ${CUDART_INC}")
 
 # -----------------------------------------------------------------------------TESTS--
 # Include testing flag(s) as precomiler

cmake/BuildTypes.cmake

@@ -3,8 +3,7 @@
 # Add -G to allow cuda-gdb to break inside kernels.
 
 if(CUDA)
-    set(EXTRA_NVCC_FLAGS " --default-stream per-thread --std=c++17")
-    set(RELION_NVCC_FLAGS "${CUDARCH} ${WARN_DBL} ${EXTRA_NVCC_FLAGS}" CACHE STRING "" FORCE)
+    set(RELION_NVCC_FLAGS "--default-stream per-thread -Xcompiler ${OpenMP_CXX_FLAGS} " CACHE STRING "" FORCE)
 elseif (HIP)
     if (${HIP_VERSION} VERSION_LESS "5.3" )
         set(EXTRA_HIPCC_FLAGS "-fgpu-default-stream=legacy -fno-gpu-rdc -munsafe-fp-atomics")
@@ -43,7 +42,7 @@ set(CMAKE_C_FLAGS_DEBUG          "${CMAKE_C_FLAGS_DEBUG} ${RELION_FLAGS_DEBUG}")
 set(CMAKE_EXE_LINKER_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS_DEBUG} ${RELION_LINKER_FLAGS_DEBUG}")
 
 if(CUDA)
-    set(CUDA_NVCC_FLAGS_DEBUG    "${RELION_NVCC_FLAGS_DEBUG}" CACHE STRING "" FORCE)
+    set(CMAKE_CUDA_FLAGS_DEBUG   "${RELION_NVCC_FLAGS_DEBUG}" CACHE STRING "" FORCE)
 elseif(HIP)
     set(CMAKE_CXX_FLAGS_DEBUG    "${CMAKE_CXX_FLAGS_DEBUG} ${RELION_HIPCC_FLAGS_DEBUG}")
 endif()
@@ -59,7 +58,7 @@ endif()
 
 # message(STATUS "Set the extra flags for Debug build type")
 # message(STATUS "RELION_NVCC_FLAGS_DEBUG : ${RELION_NVCC_FLAGS_DEBUG}")
-# message(STATUS "CUDA_NVCC_FLAGS_DEBUG : ${CUDA_NVCC_FLAGS_DEBUG}")
+# message(STATUS "CMAKE_CUDA_FLAGS_DEBUG : ${CMAKE_CUDA_FLAGS_DEBUG}")
 # message(STATUS "CMAKE_CXX_FLAGS_DEBUG : ${CMAKE_CXX_FLAGS_DEBUG}")
 #--------------------------------------------------------------------
 
@@ -82,7 +81,7 @@ set(CMAKE_CXX_FLAGS_RELWITHDEBINFO        "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${R
 set(CMAKE_C_FLAGS_RELWITHDEBINFO          "${CMAKE_C_FLAGS_RELWITHDEBINFO} ${RELION_FLAGS_RELWITHDEBINFO}")
 set(CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO "${CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO} ${RELION_LINKER_FLAGS_RELWITHDEBINFO}")
 if(CUDA)
-    set(CUDA_NVCC_FLAGS_RELWITHDEBINFO        "${RELION_NVCC_FLAGS_RELWITHDEBINFO}" CACHE STRING "" FORCE)
+    set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO       "${RELION_NVCC_FLAGS_RELWITHDEBINFO}" CACHE STRING "" FORCE)
     # -- Add preprocessor defintions ------------------------------------
     set(RELION_DEFINITIONS_RELWITHDEBINFO "-DDEBUG_CUDA")
     set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${RELION_DEFINITIONS_RELWITHDEBINFO}")
@@ -95,7 +94,7 @@ endif()
 
 # message(STATUS "Set the extra flags for RELWITHDEBINFO build type")
 # message(STATUS "RELION_NVCC_FLAGS_RELWITHDEBINFO : ${RELION_NVCC_FLAGS_RELWITHDEBINFO}")
-# message(STATUS "CUDA_NVCC_FLAGS_RELWITHDEBINFO : ${CUDA_NVCC_FLAGS_RELWITHDEBINFO}")
+# message(STATUS "CMAKE_CUDA_FLAGS_RELWITHDEBINFO : ${CMAKE_CUDA_FLAGS_RELWITHDEBINFO}")
 # message(STATUS "CMAKE_CXX_FLAGS_RELWITHDEBINFO : ${CMAKE_CXX_FLAGS_RELWITHDEBINFO}")
 #--------------------------------------------------------------------
 
@@ -130,7 +129,7 @@ set(CMAKE_CXX_FLAGS_RELEASE        "${CMAKE_CXX_FLAGS_RELEASE} ${RELION_FLAGS_RE
 set(CMAKE_C_FLAGS_RELEASE          "${CMAKE_C_FLAGS_RELEASE} ${RELION_FLAGS_RELEASE}")
 set(CMAKE_EXE_LINKER_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS_RELEASE} ${RELION_LINKER_FLAGS_RELEASE}")
 if(CUDA)
-    set(CUDA_NVCC_FLAGS_RELEASE    "${RELION_NVCC_FLAGS_RELEASE}" CACHE STRING "" FORCE)
+    set(CMAKE_CUDA_FLAGS_RELEASE   "${RELION_NVCC_FLAGS_RELEASE}" CACHE STRING "" FORCE)
 elseif(HIP)
     set(CMAKE_CXX_FLAGS_RELEASE    "${CMAKE_CXX_FLAGS_RELEASE} ${RELION_HIPCC_FLAGS_RELEASE}")
 endif()
@@ -166,7 +165,7 @@ if(CUDA)
     set(CMAKE_CXX_FLAGS_PROFILING        "${CMAKE_CXX_FLAGS_RELEASE} ${RELION_FLAGS_PROFILING}"               CACHE STRING "")
     set(CMAKE_C_FLAGS_PROFILING          "${CMAKE_C_FLAGS_RELEASE} ${RELION_FALAGS_PROFILING}"                 CACHE STRING "")
     set(CMAKE_EXE_LINKER_FLAGS_PROFILING "${CMAKE_EXE_LINKER_FLAGS_RELEASE} ${RELION_LINKER_FLAGS_PROFILING}" CACHE STRING "")
-    set(CUDA_NVCC_FLAGS_PROFILING        "${RELION_NVCC_FLAGS_PROFILING}"                                     CACHE STRING "" FORCE)
+    set(CMAKE_CUDA_FLAGS_PROFILING       "${RELION_NVCC_FLAGS_PROFILING}"                                     CACHE STRING "" FORCE)
 
     # -- Add preprocessor defintions ------------------------------------
     set(RELION_DEFINITIONS_PROFILING "-DCUDA_PROFILING")
@@ -223,7 +222,7 @@ set(CMAKE_CXX_FLAGS_BENCHMARKING        "${CMAKE_CXX_FLAGS_RELEASE} ${RELION_FLA
 set(CMAKE_C_FLAGS_BENCHMARKING          "${CMAKE_C_FLAGS_RELEASE} ${RELION_FLAGS_BENCHMARKING}"                 CACHE STRING "" FORCE)
 set(CMAKE_EXE_LINKER_FLAGS_BENCHMARKING "${CMAKE_EXE_LINKER_FLAGS_RELEASE} ${RELION_LINKER_FLAGS_BENCHMARKING}" CACHE STRING "" FORCE)
 if(CUDA)
-    set(CUDA_NVCC_FLAGS_BENCHMARKING    "${RELION_NVCC_FLAGS_BENCHMARKING}" CACHE STRING "" FORCE)
+    set(CMAKE_CUDA_FLAGS_BENCHMARKING   "${RELION_NVCC_FLAGS_BENCHMARKING}" CACHE STRING "" FORCE)
 elseif(HIP)
     set(CMAKE_CXX_FLAGS_BENCHMARKING    "${CMAKE_CXX_FLAGS_RELEASE} ${RELION_HIPCC_FLAGS_BENCHMARKING}")
 endif()

environment.yml

@@ -1,13 +1,13 @@
-name: relion-5.0
+name: relion-5.1
 channels:
   - conda-forge
 dependencies:
   - pip
   - python=3.10
   - setuptools=59.5.0
   - pip:
-      - torch==2.0.1
-      - torchvision==0.15.2
+      - --extra-index-url https://download.pytorch.org/whl/cu128
+      - torch==2.7.1+cu128
       - tqdm==4.65.0
       - mrcfile==1.4.3
       - starfile>=0.5.6
@@ -18,6 +18,8 @@ dependencies:
       - morphosamplers==0.0.13
       - pydantic==1.10.18
       - napari[all]==0.4.18
+      - napari-threedee==0.0.28
+      - psygnal==0.11.1
       - tsnecuda==3.0.1
       - PyQt5==5.15.9
       - typer==0.9.0
@@ -28,6 +30,8 @@ dependencies:
       - dill==0.3.7
       - numpy==1.26.1
       - scipy==1.11.2
+      - skan==0.12.2
+      - opencv-python==4.10.0.84
       - git+https://github.com/3dem/relion-classranker
       - git+https://github.com/3dem/relion-blush
       - git+https://github.com/3dem/DynaMight

environment_blackwell.yml → environment_pascal.yml

@@ -1,14 +1,12 @@
-name: relion-5.0
+name: relion-5.1
 channels:
   - conda-forge
 dependencies:
   - pip
   - python=3.10
   - setuptools=59.5.0
   - pip:
-      - --extra-index-url https://download.pytorch.org/whl/cu128
-      - torch==2.7.1+cu128
-      - torchvision==0.22.1+cu128
+      - torch==2.0.1
       - tqdm==4.65.0
       - mrcfile==1.4.3
       - starfile>=0.5.6
@@ -29,6 +27,8 @@ dependencies:
       - dill==0.3.7
       - numpy==1.26.1
       - scipy==1.11.2
+      - skan==0.12.2
+      - opencv-python==4.10.0.84
       - git+https://github.com/3dem/relion-classranker
       - git+https://github.com/3dem/relion-blush
       - git+https://github.com/3dem/DynaMight