Added CMake support for cross platform compile

.gitignore

@@ -4,9 +4,15 @@
 .settings
 
 *.pyc
+*.pyd
 
 *.o
 *.so
 *.a
+*.dll
+*.lib
 
-*~
+*~
+
+/build
+/python

CMakeLists.txt

@@ -0,0 +1,62 @@
+cmake_minimum_required (VERSION 2.8.3)
+project (DenseInferenceWrapper)
+
+if(POLICY CMP0020)
+  cmake_policy(SET CMP0020 NEW)
+endif()
+
+set(CMAKE_BUILD_TYPE Release)
+
+#python
+find_package(PythonLibs REQUIRED)
+include_directories(${PYTHON_INCLUDE_DIRS})
+
+# include_directories(${CMAKE_BINARY_DIR})
+
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_SOURCE_DIR}/lib)
+set(CMAKE_BINARY_DIR ${PROJECT_SOURCE_DIR}/bin)
+
+link_directories(${PROJECT_SOURCE_DIR}/lib)
+add_subdirectory(denseinference)
+
+# SET(
+# 	CXX_SRC
+# 	${CMAKE_SOURCE_DIR}/codes/cxx/main.cxx
+# 	)
+
+# SET(
+# 	CXX_HDR
+# 	)
+
+# SET(Python_SRC_DIR ${CMAKE_SOURCE_DIR}/codes/python)
+
+# FILE(GLOB Python_SRC ${Python_SRC_DIR}/*.py)
+
+# add_executable(PythonCxxEmbedding ${CXX_SRC} ${Python_SRC})
+# target_link_libraries(PythonCxxEmbedding ${PYTHON_LIBRARIES})
+
+# #Grouping in MSVC
+# SOURCE_GROUP("Headers" FILES ${CXX_HDR})
+# SOURCE_GROUP("Sources" FILES ${CXX_SRC})
+# SOURCE_GROUP("Python Sources" FILES ${Python_SRC})
+
+# #copy python files to build directory
+# macro(copy_python_files srcDir destDir)
+#     message(STATUS "Configuring python files")
+#     make_directory(${destDir})
+
+#     file(GLOB templateFiles RELATIVE ${srcDir} ${srcDir}/*)
+#     foreach(templateFile ${templateFiles})
+#         set(srcTemplatePath ${srcDir}/${templateFile})
+#         if(NOT IS_DIRECTORY ${srcTemplatePath})
+#             # message(STATUS "Configuring file ${templateFile}")
+#             configure_file(
+#                     ${srcTemplatePath}
+#                     ${destDir}/${templateFile}
+#                     @ONLY)
+#         endif(NOT IS_DIRECTORY ${srcTemplatePath})
+#     endforeach(templateFile)
+# endmacro(copy_python_files)
+
+# copy_python_files(${Python_SRC_DIR} ${CMAKE_BINARY_DIR}/Debug)
+# copy_python_files(${Python_SRC_DIR} ${CMAKE_BINARY_DIR}/RELEASE)

denseinference/CMakeLists.txt

@@ -0,0 +1 @@
+add_subdirectory(lib)

denseinference/CRFProcessor.py

@@ -1,11 +1,10 @@
-__author__ = 'Marc Bickel'
+__author__ = 'Marc Bickel, modified by Jacky Ko'
 
 import numpy as np
 import psutil
 
 from denseinference.lib import dense_inference as di
 
-
 class CRF3DProcessor(object):
     # #
     #

denseinference/lib/CMakeLists.txt

@@ -0,0 +1,3 @@
+add_subdirectory(libDenseCRF)
+add_subdirectory(refine_3d)
+

denseinference/lib/Makefile

@@ -1,7 +1,7 @@
 # update the path variables 
 
 CC	= g++
-CFLAGS	= -W -Wall -O2 -DNDEBUG
+CFLAGS	= -W -Wall -O2 -DNDEBUG	
 #CFLAGS	= -W -Wall -g
 LIB_ROOT = denseinference/lib/
 

denseinference/lib/libDenseCRF/CMakeLists.txt

@@ -0,0 +1,20 @@
+cmake_minimum_required (VERSION 2.8.3)
+project(libDenseCRF)
+
+MESSAGE(STATUS "Configuring ${PROJECT_NAME}...")
+
+if(POLICY CMP0020)
+  cmake_policy(SET CMP0020 NEW)
+endif()
+
+set(CMAKE_BUILD_TYPE Release)
+
+#python
+find_package(PythonLibs REQUIRED)
+include_directories(${PYTHON_INCLUDE_DIRS})
+
+FILE(GLOB LibDenseCRF_SRC *.cpp)
+FILE(GLOB LibDenseCRF_HDR *.h)
+
+add_library(${PROJECT_NAME} STATIC ${LibDenseCRF_SRC} ${LibDenseCRF_HDR})
+target_link_libraries(${PROJECT_NAME})

denseinference/lib/libDenseCRF/permutohedral.h

@@ -46,11 +46,11 @@
 # endif
 #endif
 
-#ifdef WIN32
-static float round( float v ) {
-  return floor( v+0.5f );
-}
-#endif
+//#ifdef WIN32
+//static float round( float v ) {
+//  return floor( v+0.5f );
+//}
+//#endif
 
 /************************************************/
 /***                Hash Table                ***/

denseinference/lib/refine_3d/CMakeLists.txt

@@ -0,0 +1,37 @@
+cmake_minimum_required (VERSION 3.3)
+project(dense_inference)
+
+MESSAGE(STATUS "Configuring ${PROJECT_NAME}...")
+
+if(POLICY CMP0020)
+  cmake_policy(SET CMP0020 NEW)
+endif()
+
+set(CMAKE_BUILD_TYPE Release)
+
+#python
+# SET(Python_ADDITIONAL_VERSIONS 3)
+FIND_PACKAGE(PythonInterp REQUIRED)
+find_package(PythonLibs REQUIRED)
+include_directories(${PYTHON_INCLUDE_DIRS})
+get_filename_component(Python_Root ${PYTHON_EXECUTABLE} DIRECTORY)
+
+#FindBoost
+find_package(Boost COMPONENTS python REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+
+FILE(GLOB DenseInference_SRC *.cpp)
+FILE(GLOB DenseInference_HDR *.h)
+
+# numpy
+SET(NUMPY_INCLUDE "${Python_Root}/Lib/site-packages/numpy/core/include" CACHE PATH "Path to numpy include folder")
+if(NOT NUMPY_INCLUDE)
+    message(FATAL_ERROR "numpy is not found")
+endif()
+include_directories(${NUMPY_INCLUDE})
+
+include_directories(${CMAKE_SOURCE_DIR})
+
+
+add_library(${PROJECT_NAME} SHARED ${DenseInference_SRC} ${DenseInference_HDR})
+target_link_libraries(${PROJECT_NAME} ${PYTHON_LIBRARY} ${Boost_LIBRARIES} libDenseCRF)

readme.md

@@ -22,7 +22,7 @@ for more information.
 #### Requirements
 
 ```
-make, g++, boost-python
+make, g++, boost-python, cmake, python 2 (python 3 has been tested with compilation fail), MSVC2015 (for windows)
 ```
 
 #### Requirements Python
@@ -35,14 +35,33 @@ numpy, psutil
 matplotlib
 ```
 
-#### Installation
+#### Installation (Linux)
 
 ```bash
 cd denseinferencewrapper
 make all
 sudo pip install .
 ```
 
+#### CMake Installation (Tested on Windows with MSVC2015)
+```
+1. Create a build folder anywhere
+2. CMake with specifying source and build folder
+3. Configure (Python, Boost, Numpy)
+4. Generate
+5. build 
+	- Windows
+		1. Open .sln file in build folder
+		2. Build Release version
+		3. Copy <build-folder>/build/denseinference/lib/refine_3d/Release/dense_inference.dll (.so for linux) to <source-folder>/denseinference/lib
+		4. Rename the extension from .dll/.so to .pyd
+	- Linux
+		(To be updated...)
+8. Open CMD/Terminal at <source-folder>
+9. pip install . (Permission error will occur if .sln file is open)
+10. Copy boost_python-vc140-mt-1_64.dll (.so for linux) at <boost-dir>/lib64-msvc-14.0 to <python-dir>/Lib/site-packages/denseinference/lib
+```
+
 ## Usage
 
 ```python
@@ -74,4 +93,4 @@ result = pro.set_data_and_run(img, feature_tensor)
 
 - **param img**: Normalized input as ndarray. (W, H, D), [0, 1]  
 - **param label**: Continuous label tensor as ndarray. (W, H, D, L), [0, 1]  
-- **return**: Hard labeled result as ndarray. (W, H, D), [0, L], dtype=int16  
+- **return**: Hard labeled result as ndarray. (W, H, D), [0, L], dtype=int16  

setup.py

@@ -1,13 +1,17 @@
 from setuptools import setup, find_packages
+from sys import platform
+
+package_data = 'lib/dense_inference.pyd'
+
 setup(
     name="DenseInferenceWrapper",
     version="1.0.0",
     packages=find_packages(),
-    package_data={'': ['lib/dense_inference.so']},
+    package_data={'': [package_data]},
     include_package_data=True,
     url='',
     license='',
-    author='Marc Bickel',
-    author_email='marc.bickel@mytum.de',
+    author='Marc Bickel, Jacky Ko',
+    author_email='marc.bickel@mytum.de, jackkykokoko@gmail.com',
     description='Wrapper for Kraehenbuehls DenseCRF for 3D image data.'
 )