release / siproc

Commit 18c1cc40ccfdfae7ee7a43d4443230a7cb559a03

Authored by David Mayerich
1 parent 15dbd763

Updated SIproc for vcpkg

Showing 10 changed files with 174 additions and 599 deletions   Show diff stats
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@@ -64,14 +64,15 @@ if(WIN32) @@ -64,14 +64,15 @@ if(WIN32)
64 endif(WIN32) 64 endif(WIN32)
65 65
66 #find LAPACK and supporting link_libraries 66 #find LAPACK and supporting link_libraries
67 -find_package(LAPACKE REQUIRED) 67 +find_package(clapack CONFIG REQUIRED)
  68 +find_package(OpenBLAS CONFIG REQUIRED)
68 #if(MSVC) 69 #if(MSVC)
69 # message("Warning: VS2015 made a change to printf and scanf functions that requires linking to legacy_stdio_definitions.lib") 70 # message("Warning: VS2015 made a change to printf and scanf functions that requires linking to legacy_stdio_definitions.lib")
70 #endif() 71 #endif()
71 72
72 #include include directories 73 #include include directories
73 include_directories(${CUDA_INCLUDE_DIRS} 74 include_directories(${CUDA_INCLUDE_DIRS}
74 - ${LAPACKE_INCLUDE_DIR} 75 + ${CLAPACK_INCLUDE_DIR}
75 ${STIM_INCLUDE_DIRS} 76 ${STIM_INCLUDE_DIRS}
76 ${OpenGL_INCLUDE_DIRS} 77 ${OpenGL_INCLUDE_DIRS}
77 ${GLUT_INCLUDE_DIR} 78 ${GLUT_INCLUDE_DIR}
@@ -96,9 +97,11 @@ add_executable(siproc @@ -96,9 +97,11 @@ add_executable(siproc
96 target_link_libraries(siproc ${CUDA_LIBRARIES} 97 target_link_libraries(siproc ${CUDA_LIBRARIES}
97 ${CUDA_CUBLAS_LIBRARIES} 98 ${CUDA_CUBLAS_LIBRARIES}
98 ${CUDA_CUFFT_LIBRARIES} 99 ${CUDA_CUFFT_LIBRARIES}
99 - ${LAPACKE_LIBRARIES} 100 + ${CLAPACK_LIBRARIES}
100 ${CMAKE_THREAD_LIBS_INIT} 101 ${CMAKE_THREAD_LIBS_INIT}
101 ${X11_LIBRARIES} 102 ${X11_LIBRARIES}
  103 + OpenBLAS::OpenBLAS
  104 + f2c lapack
102 ) 105 )
103 106
104 #create the VIEW executable---------------------------------------------- 107 #create the VIEW executable----------------------------------------------
@@ -112,7 +115,7 @@ target_link_libraries(siview @@ -112,7 +115,7 @@ target_link_libraries(siview
112 ${GLUT_LIBRARIES} 115 ${GLUT_LIBRARIES}
113 ) 116 )
114 if(WIN32) 117 if(WIN32)
115 - target_link_libraries(siview ${GLEW_GLEW_LIBRARY}) 118 + target_link_libraries(siview ${GLEW_LIBRARIES})
116 endif(WIN32) 119 endif(WIN32)
117 120
118 #create instrument-specific subroutine executables 121 #create instrument-specific subroutine executables
@@ -140,7 +143,7 @@ target_link_libraries(spero @@ -140,7 +143,7 @@ target_link_libraries(spero
140 #if Boost is found, set an environment variable to use with preprocessor directives 143 #if Boost is found, set an environment variable to use with preprocessor directives
141 if(Boost_FILESYSTEM_FOUND) 144 if(Boost_FILESYSTEM_FOUND)
142 target_link_libraries(siproc ${Boost_FILESYSTEM_LIBRARIES} 145 target_link_libraries(siproc ${Boost_FILESYSTEM_LIBRARIES}
143 - ${Boost_SYSTEM_LIBRARY} 146 + ${Boost_SYSTEM_LIBRARY}
144 ) 147 )
145 target_link_libraries(siview 148 target_link_libraries(siview
146 ${Boost_FILESYSTEM_LIBRARIES} 149 ${Boost_FILESYSTEM_LIBRARIES}
FindFANN.cmake deleted
View file @15dbd76
1 -#  
2 -# Windows users: define the GLEW_PATH environment variable to point  
3 -# to the directory containing:  
4 -# include/fann.h  
5 -# lib/*fann.lib  
6 -  
7 -  
8 -# FANN_FOUND - system has fann  
9 -# FANN_INCLUDE_DIRS - the fann include directory  
10 -# FANN_LIBRARIES - Link these to use fann  
11 -# FANN_DEFINITIONS - Compiler switches required for using fann  
12 -#  
13 -  
14 -if(FANN_LIBRARIES AND FANN_INCLUDE_DIRS)  
15 - set(FANN_FOUND TRUE)  
16 -else()  
17 - find_path(FANN_INCLUDE_DIR  
18 - NAMES  
19 - fann.h  
20 - PATHS  
21 - $ENV{FANN_PATH}/include  
22 - ${FANN_DIR}/include  
23 - /usr/include  
24 - /usr/local/include  
25 - /opt/local/include  
26 - /sw/include  
27 - )  
28 -  
29 - set( _libraries doublefann floatfann )  
30 -  
31 - foreach( _lib ${_libraries} )  
32 - string( TOUPPER ${_lib} _name )  
33 -  
34 - find_library(${_name}_LIBRARY  
35 - NAMES  
36 - ${_lib}  
37 - PATHS  
38 - $ENV{FANN_PATH}/lib  
39 - ${FANN_DIR}/lib  
40 - /usr/lib  
41 - /usr/local/lib  
42 - /opt/local/lib  
43 - /sw/lib  
44 - )  
45 - endforeach()  
46 -  
47 -  
48 - set(FANN_INCLUDE_DIRS  
49 - ${FANN_INCLUDE_DIR}  
50 - )  
51 -  
52 - set(FANN_LIBRARIES  
53 - ${FANN_LIBRARIES}  
54 - ${FANN_LIBRARY}  
55 - ${DOUBLEFANN_LIBRARY}  
56 - ${FIXEDFANN_LIBRARY}  
57 - ${FLOATFANN_LIBRARY}  
58 - )  
59 -  
60 - if( UNIX )  
61 - set( FANN_LIBRARIES ${FANN_LIBRARIES} m )  
62 - endif()  
63 -  
64 - if(FANN_INCLUDE_DIRS AND FANN_LIBRARIES)  
65 - set(FANN_FOUND TRUE)  
66 - endif()  
67 -  
68 - if(FANN_FOUND)  
69 - if(NOT FANN_FIND_QUIETLY)  
70 - message(STATUS "Found FANN")  
71 - #message(STATUS "FANN_INCLUDE_DIRS: ${FANN_INCLUDE_DIRS}")  
72 - #message(STATUS "FANN_LIBRARIES: ${FANN_LIBRARIES}")  
73 - endif()  
74 - else()  
75 - if(FANN_FIND_REQUIRED)  
76 - message(FATAL_ERROR "Could not find FANN")  
77 - endif()  
78 - endif()  
79 -  
80 - mark_as_advanced(FANN_INCLUDE_DIRS FANN_LIBRARIES)  
81 -endif()  
FindGLEW.cmake deleted
View file @15dbd76
1 -# Copyright (c) 2012-2016 DreamWorks Animation LLC  
2 -#  
3 -# All rights reserved. This software is distributed under the  
4 -# Mozilla Public License 2.0 ( http://www.mozilla.org/MPL/2.0/ )  
5 -#  
6 -# Redistributions of source code must retain the above copyright  
7 -# and license notice and the following restrictions and disclaimer.  
8 -#  
9 -# * Neither the name of DreamWorks Animation nor the names of  
10 -# its contributors may be used to endorse or promote products derived  
11 -# from this software without specific prior written permission.  
12 -#  
13 -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS  
14 -# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT  
15 -# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR  
16 -# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT  
17 -# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY INDIRECT, INCIDENTAL,  
18 -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT  
19 -# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,  
20 -# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY  
21 -# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT  
22 -# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE  
23 -# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.  
24 -# IN NO EVENT SHALL THE COPYRIGHT HOLDERS' AND CONTRIBUTORS' AGGREGATE  
25 -# LIABILITY FOR ALL CLAIMS REGARDLESS OF THEIR BASIS EXCEED US$250.00.  
26 -#  
27 -  
28 -#-*-cmake-*-  
29 -# - Find GLEW  
30 -#  
31 -# Author : Nicholas Yue yue.nicholas@gmail.com  
32 -#  
33 -# This auxiliary CMake file helps in find the GLEW headers and libraries  
34 -#  
35 -# GLEW_FOUND set if Glew is found.  
36 -# GLEW_INCLUDE_DIR GLEW's include directory  
37 -# GLEW_GLEW_LIBRARY GLEW libraries  
38 -# GLEW_glewmx_LIBRARY GLEWmx libraries (Mulitple Rendering Context)  
39 -  
40 -FIND_PACKAGE ( PackageHandleStandardArgs )  
41 -  
42 -FIND_PATH( GLEW_LOCATION include/GL/glew.h  
43 - "$ENV{GLEW_ROOT}"  
44 - NO_DEFAULT_PATH  
45 - NO_SYSTEM_ENVIRONMENT_PATH  
46 - )  
47 -  
48 -FIND_PACKAGE_HANDLE_STANDARD_ARGS ( GLEW  
49 - REQUIRED_VARS GLEW_LOCATION  
50 - )  
51 -  
52 -IF ( GLEW_LOCATION )  
53 - SET( GLEW_INCLUDE_DIR "${GLEW_LOCATION}/include" CACHE STRING "GLEW include path")  
54 -  
55 - SET ( ORIGINAL_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES})  
56 - IF (GLEW_USE_STATIC_LIBS)  
57 - IF (APPLE)  
58 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")  
59 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW PATHS ${GLEW_LOCATION}/lib  
60 - NO_DEFAULT_PATH  
61 - NO_SYSTEM_ENVIRONMENT_PATH  
62 - )  
63 - FIND_LIBRARY ( GLEWmx_LIBRARY_PATH GLEWmx PATHS ${GLEW_LOCATION}/lib  
64 - NO_DEFAULT_PATH  
65 - NO_SYSTEM_ENVIRONMENT_PATH  
66 - )  
67 - # MESSAGE ( "APPLE STATIC" )  
68 - # MESSAGE ( "GLEW_LIBRARY_PATH = " ${GLEW_LIBRARY_PATH} )  
69 - ELSEIF (WIN32)  
70 - message("Windows Found!")  
71 - # Link library  
72 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib")  
73 - if( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
74 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW32S PATHS $ENV{GLEW_ROOT}/lib/x64 NO_DEFAULT_PATH)  
75 - message("64-bit library")  
76 - else( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
77 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW32S PATHS $ENV{GLEW_ROOT}/lib NO_DEFAULT_PATH)  
78 - message("32-bit library")  
79 - endif( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
80 - ELSE (APPLE)  
81 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ".a")  
82 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW PATHS ${GLEW_LOCATION}/lib  
83 - NO_DEFAULT_PATH  
84 - NO_SYSTEM_ENVIRONMENT_PATH  
85 - )  
86 - FIND_LIBRARY ( GLEWmx_LIBRARY_PATH GLEWmx PATHS ${GLEW_LOCATION}/lib  
87 - NO_DEFAULT_PATH  
88 - NO_SYSTEM_ENVIRONMENT_PATH  
89 - )  
90 - # MESSAGE ( "LINUX STATIC" )  
91 - # MESSAGE ( "GLEW_LIBRARY_PATH = " ${GLEW_LIBRARY_PATH} )  
92 - ENDIF (APPLE)  
93 - ELSE ()  
94 - IF (APPLE)  
95 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ".dylib")  
96 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW PATHS ${GLEW_LOCATION}/lib )  
97 - FIND_LIBRARY ( GLEWmx_LIBRARY_PATH GLEWmx PATHS ${GLEW_LOCATION}/lib )  
98 - ELSEIF (WIN32)  
99 - # Link library  
100 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib")  
101 - if( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
102 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW32S PATHS $ENV{GLEW_ROOT}/lib/x64 NO_DEFAULT_PATH)  
103 - else( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
104 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW32S PATHS $ENV{GLEW_ROOT}/lib NO_DEFAULT_PATH)  
105 - endif( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
106 - ELSE (APPLE)  
107 - # Unices  
108 - FIND_LIBRARY ( GLEW_LIBRARY_PATH GLEW PATHS ${GLEW_LOCATION}/lib  
109 - NO_DEFAULT_PATH  
110 - NO_SYSTEM_ENVIRONMENT_PATH  
111 - )  
112 - FIND_LIBRARY ( GLEWmx_LIBRARY_PATH GLEWmx PATHS ${GLEW_LOCATION}/lib  
113 - NO_DEFAULT_PATH  
114 - NO_SYSTEM_ENVIRONMENT_PATH  
115 - )  
116 - ENDIF (APPLE)  
117 - ENDIF ()  
118 - # MUST reset  
119 - SET(CMAKE_FIND_LIBRARY_SUFFIXES ${ORIGINAL_CMAKE_FIND_LIBRARY_SUFFIXES})  
120 -  
121 - SET( GLEW_GLEW_LIBRARY ${GLEW_LIBRARY_PATH} CACHE STRING "GLEW library")  
122 - SET( GLEW_GLEWmx_LIBRARY ${GLEWmx_LIBRARY_PATH} CACHE STRING "GLEWmx library")  
123 -  
124 -ENDIF ()  
FindGLUT.cmake deleted
View file @15dbd76
1 -#.rst:  
2 -# FindGLUT  
3 -# --------  
4 -#  
5 -# try to find glut library and include files.  
6 -#  
7 -# IMPORTED Targets  
8 -# ^^^^^^^^^^^^^^^^  
9 -#  
10 -# This module defines the :prop_tgt:`IMPORTED` targets:  
11 -#  
12 -# ``GLUT::GLUT``  
13 -# Defined if the system has GLUT.  
14 -#  
15 -# Result Variables  
16 -# ^^^^^^^^^^^^^^^^  
17 -#  
18 -# This module sets the following variables:  
19 -#  
20 -# ::  
21 -#  
22 -# GLUT_INCLUDE_DIR, where to find GL/glut.h, etc.  
23 -# GLUT_LIBRARIES, the libraries to link against  
24 -# GLUT_FOUND, If false, do not try to use GLUT.  
25 -#  
26 -# Also defined, but not for general use are:  
27 -#  
28 -# ::  
29 -#  
30 -# GLUT_glut_LIBRARY = the full path to the glut library.  
31 -# GLUT_Xmu_LIBRARY = the full path to the Xmu library.  
32 -# GLUT_Xi_LIBRARY = the full path to the Xi Library.  
33 -  
34 -#=============================================================================  
35 -# Copyright 2001-2009 Kitware, Inc.  
36 -#  
37 -# Distributed under the OSI-approved BSD License (the "License");  
38 -# see accompanying file Copyright.txt for details.  
39 -#  
40 -# This software is distributed WITHOUT ANY WARRANTY; without even the  
41 -# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
42 -# See the License for more information.  
43 -#=============================================================================  
44 -# (To distribute this file outside of CMake, substitute the full  
45 -# License text for the above reference.)  
46 -  
47 -if (WIN32)  
48 - find_path( GLUT_INCLUDE_DIR NAMES GL/glut.h  
49 - PATHS $ENV{GLUT_ROOT}/include)  
50 -  
51 - if( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
52 - find_library( GLUT_glut_LIBRARY NAMES freeglut  
53 - PATHS  
54 - $ENV{GLUT_ROOT}/lib/x64  
55 -  
56 - NO_DEFAULT_PATH  
57 - )  
58 - else( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
59 - find_library( GLUT_glut_LIBRARY NAMES glut glut32 freeglut  
60 - PATHS  
61 - $ENV{GLUT_ROOT}/lib  
62 - )  
63 - endif( CMAKE_SIZEOF_VOID_P EQUAL 8 )  
64 -  
65 -else ()  
66 -  
67 - if (APPLE)  
68 - find_path(GLUT_INCLUDE_DIR glut.h ${OPENGL_LIBRARY_DIR})  
69 - find_library(GLUT_glut_LIBRARY GLUT DOC "GLUT library for OSX")  
70 - find_library(GLUT_cocoa_LIBRARY Cocoa DOC "Cocoa framework for OSX")  
71 -  
72 - if(GLUT_cocoa_LIBRARY AND NOT TARGET GLUT::Cocoa)  
73 - add_library(GLUT::Cocoa UNKNOWN IMPORTED)  
74 - # Cocoa should always be a Framework, but we check to make sure.  
75 - if(GLUT_cocoa_LIBRARY MATCHES "/([^/]+)\\.framework$")  
76 - set_target_properties(GLUT::Cocoa PROPERTIES  
77 - IMPORTED_LOCATION "${GLUT_cocoa_LIBRARY}/${CMAKE_MATCH_1}")  
78 - else()  
79 - set_target_properties(GLUT::Cocoa PROPERTIES  
80 - IMPORTED_LOCATION "${GLUT_cocoa_LIBRARY}")  
81 - endif()  
82 - endif()  
83 - else ()  
84 -  
85 - if (BEOS)  
86 -  
87 - set(_GLUT_INC_DIR /boot/develop/headers/os/opengl)  
88 - set(_GLUT_glut_LIB_DIR /boot/develop/lib/x86)  
89 -  
90 - else()  
91 -  
92 - find_library( GLUT_Xi_LIBRARY Xi  
93 - /usr/openwin/lib  
94 - )  
95 -  
96 - find_library( GLUT_Xmu_LIBRARY Xmu  
97 - /usr/openwin/lib  
98 - )  
99 -  
100 - if(GLUT_Xi_LIBRARY AND NOT TARGET GLUT::Xi)  
101 - add_library(GLUT::Xi UNKNOWN IMPORTED)  
102 - set_target_properties(GLUT::Xi PROPERTIES  
103 - IMPORTED_LOCATION "${GLUT_Xi_LIBRARY}")  
104 - endif()  
105 -  
106 - if(GLUT_Xmu_LIBRARY AND NOT TARGET GLUT::Xmu)  
107 - add_library(GLUT::Xmu UNKNOWN IMPORTED)  
108 - set_target_properties(GLUT::Xmu PROPERTIES  
109 - IMPORTED_LOCATION "${GLUT_Xmu_LIBRARY}")  
110 - endif()  
111 -  
112 - endif ()  
113 -  
114 - find_path( GLUT_INCLUDE_DIR GL/glut.h  
115 - /usr/include/GL  
116 - /usr/openwin/share/include  
117 - /usr/openwin/include  
118 - /opt/graphics/OpenGL/include  
119 - /opt/graphics/OpenGL/contrib/libglut  
120 - ${_GLUT_INC_DIR}  
121 - )  
122 -  
123 - find_library( GLUT_glut_LIBRARY glut  
124 - /usr/openwin/lib  
125 - ${_GLUT_glut_LIB_DIR}  
126 - )  
127 -  
128 - unset(_GLUT_INC_DIR)  
129 - unset(_GLUT_glut_LIB_DIR)  
130 -  
131 - endif ()  
132 -  
133 -endif ()  
134 -  
135 -FIND_PACKAGE_HANDLE_STANDARD_ARGS(GLUT REQUIRED_VARS GLUT_glut_LIBRARY GLUT_INCLUDE_DIR)  
136 -  
137 -if (GLUT_FOUND)  
138 - # Is -lXi and -lXmu required on all platforms that have it?  
139 - # If not, we need some way to figure out what platform we are on.  
140 - set( GLUT_LIBRARIES  
141 - ${GLUT_glut_LIBRARY}  
142 - ${GLUT_Xmu_LIBRARY}  
143 - ${GLUT_Xi_LIBRARY}  
144 - ${GLUT_cocoa_LIBRARY}  
145 - )  
146 -  
147 - if(NOT TARGET GLUT::GLUT)  
148 - add_library(GLUT::GLUT UNKNOWN IMPORTED)  
149 - set_target_properties(GLUT::GLUT PROPERTIES  
150 - INTERFACE_INCLUDE_DIRECTORIES "${GLUT_INCLUDE_DIR}")  
151 - if(GLUT_glut_LIBRARY MATCHES "/([^/]+)\\.framework$")  
152 - set_target_properties(GLUT::GLUT PROPERTIES  
153 - IMPORTED_LOCATION "${GLUT_glut_LIBRARY}/${CMAKE_MATCH_1}")  
154 - else()  
155 - set_target_properties(GLUT::GLUT PROPERTIES  
156 - IMPORTED_LOCATION "${GLUT_glut_LIBRARY}")  
157 - endif()  
158 -  
159 - if(TARGET GLUT::Xmu)  
160 - set_property(TARGET GLUT::GLUT APPEND  
161 - PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Xmu)  
162 - endif()  
163 -  
164 - if(TARGET GLUT::Xi)  
165 - set_property(TARGET GLUT::GLUT APPEND  
166 - PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Xi)  
167 - endif()  
168 -  
169 - if(TARGET GLUT::Cocoa)  
170 - set_property(TARGET GLUT::GLUT APPEND  
171 - PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Cocoa)  
172 - endif()  
173 - endif()  
174 -  
175 - #The following deprecated settings are for backwards compatibility with CMake1.4  
176 - set (GLUT_LIBRARY ${GLUT_LIBRARIES})  
177 - set (GLUT_INCLUDE_PATH ${GLUT_INCLUDE_DIR})  
178 -endif()  
179 -  
180 -mark_as_advanced(  
181 - GLUT_INCLUDE_DIR  
182 - GLUT_glut_LIBRARY  
183 - GLUT_Xmu_LIBRARY  
184 - GLUT_Xi_LIBRARY  
185 - )  
FindLAPACKE.cmake deleted
View file @15dbd76
1 -# - Try to find LAPACKE  
2 -#  
3 -# Once done this will define  
4 -# LAPACKE_FOUND - System has LAPACKE  
5 -# LAPACKE_INCLUDE_DIRS - The LAPACKE include directories  
6 -# LAPACKE_LIBRARIES - The libraries needed to use LAPACKE  
7 -# LAPACKE_DEFINITIONS - Compiler switches required for using LAPACKE  
8 -#  
9 -# Usually, LAPACKE requires LAPACK and the BLAS. This module does  
10 -# not enforce anything about that.  
11 -  
12 -find_path(LAPACKE_INCLUDE_DIR  
13 - NAMES lapacke.h  
14 - PATHS $ENV{LAPACK_ROOT} $ENV{LAPACK_PATH} ${INCLUDE_INSTALL_DIR}  
15 - PATHS ENV INCLUDE)  
16 -  
17 -find_library(LAPACKE_LIBRARY liblapacke lapacke  
18 - PATHS $ENV{LAPACK_ROOT} $ENV{LAPACK_PATH} ${LIB_INSTALL_DIR}  
19 - PATHS ENV LIBRARY_PATH  
20 - PATHS ENV LD_LIBRARY_PATH)  
21 -  
22 -if(MSVC)  
23 - find_library(LAPACK_LIBRARY liblapack lapack  
24 - PATHS $ENV{LAPACK_ROOT} $ENV{LAPACK_PATH} ${LIB_INSTALL_DIR}  
25 - PATHS ENV LIBRARY_PATH  
26 - PATHS ENV LD_LIBRARY_PATH)  
27 -  
28 - find_library(BLAS_LIBRARY libblas blas  
29 - PATHS $ENV{LAPACK_ROOT} $ENV{LAPACK_PATH} ${LIB_INSTALL_DIR}  
30 - PATHS ENV LIBRARY_PATH  
31 - PATHS ENV LD_LIBRARY_PATH)  
32 -  
33 -else()  
34 - find_library(LAPACK REQUIRED)  
35 - find_library(BLAS REQUIRED)  
36 -endif()  
37 -set(LAPACKE_LIBRARIES ${LAPACKE_LIBRARY} ${LAPACK_LIBRARY} ${BLAS_LIBRARY})  
38 -  
39 -include(FindPackageHandleStandardArgs)  
40 -find_package_handle_standard_args(LAPACKE DEFAULT_MSG  
41 - LAPACKE_INCLUDE_DIR  
42 - LAPACKE_LIBRARIES)  
43 -mark_as_advanced(LAPACKE_INCLUDE_DIR LAPACKE_LIBRARIES)  
1 -HSIproc can be built using CMake (https://cmake.org/) and a C/C++ compiler.  
2 -  
3 -The STIM codebase is required, but will be cloned automatically if Git (https://git-scm.com/) is installed. The codebase can be downloaded manually here:  
4 -https://git.stim.ee.uh.edu/codebase/stimlib  
5 -  
6 -Required libraries:  
7 -OpenCV: http://opencv.org/  
8 -  
9 -  
10 -  
11 ------------------------------------------------------------------------  
12 -Step-by-step instructions:  
13 -  
14 -1) Download and install CMake  
15 -  
16 -2) Download and install OpenCV  
17 -  
18 -3) Download and install Git  
19 -  
20 -4) Set the CMake source directory to the directory containing this file  
21 -  
22 -5) Specify the CMake build directory where you want the executable built  
23 -  
24 -6) Use CMake to Configure and Generate the build environment  
25 -  
26 -7) Build the software (ex. in Visual Studio you will open the generated solution and compile) 1 +SIproc is written using C++ and compatible with both CMake (https://cmake.org/) and the vcpkg (https://docs.microsoft.com/en-us/cpp/build/vcpkg) package manager.
  2 +
  3 +STIM (https://git.stim.ee.uh.edu/codebase/stimlib) is also required.
  4 +
  5 +Step-by-step instructions (Windows):
  6 +=============
  7 +1) Download and install CMake (https://cmake.org/)
  8 +2) Download and install Git (https://git-scm.com/)
  9 +3) Download and install vcpkg (https://github.com/microsoft/vcpkg):
  10 +
  11 + git clone https://github.com/Microsoft/vcpkg.git
  12 + cd vcpkg
  13 +4) Install the required packages:
  14 +
  15 + vcpkg install boost:x64-windows
  16 + vcpkg install glew:x64-windows
  17 + vcpkg install freeglut:x64-windows
  18 + vcpkg install clapack:x64-windows
  19 +5) Clone SIproc:
  20 +
  21 + git clone https://git.stim.ee.uh.edu/release/siproc.git
  22 +6) Run CMake, and select the cloned siproc directory and your choice of build location
  23 +7) Configure the build environment:
  24 +a) Click __Configure__
  25 +b) Select your preferred build environment (ex. Visual Studio)
  26 +c) Set the platform to __x64__
  27 +d) Select the option to __Specify toolchain file for cross-compiling__
  28 +e) Click __ Next__
  29 +f) When asked, provide the vcpkg toolchain file in:
  30 +
  31 + [vcpkg directory]\scripts\buildsystems\vcpkg.cmake
  32 +g) Assuming no errors were encountered, click __Generate__
  33 +8) Click __Open Project__ to open your build environment
  34 +9) Build the project (ex. Visual Studio's __Build Project__)
  35 +
src/linalg.cpp 0 → 100644
  Show/Hide comments   View file @18c1cc4
  1 +
  2 +// This file contains a set of wrapper functions that are linked to the corresponding functions in CLAPACK
  3 +
  4 +extern "C" {
  5 +#include "f2c.h"
  6 +#include "clapack.h"
  7 +}
  8 +
  9 +void LINALG_dgeev(
  10 + char JOBVL,
  11 + char JOBVR,
  12 + int n,
  13 + double* A,
  14 + int LDA,
  15 + double* WR,
  16 + double* WI,
  17 + double* VL,
  18 + int LDVL,
  19 + double* VR,
  20 + int LDVR)
  21 +{
  22 + integer LWORK = -1;
  23 + double WORK[1];
  24 + integer INFO;
  25 + dgeev_(&JOBVL, &JOBVR, (integer*)&n, A, (integer*)&LDA, WR, WI, VL, (integer*)&LDVL, VR, (integer*)&LDVR, WORK, &LWORK, &INFO);
  26 +}
  27 +
  28 +void LINALG_dgetrf(
  29 + int M,
  30 + int N,
  31 + double* A,
  32 + int LDA,
  33 + int* IPIV)
  34 +{
  35 + integer INFO;
  36 + dgetrf_((integer*)&M, (integer*)&N, A, (integer*)&LDA, (integer*)IPIV, &INFO);
  37 +}
  38 +
  39 +void LINALG_dgetri(
  40 + int N,
  41 + double* A,
  42 + int LDA,
  43 + int* IPIV)
  44 +{
  45 + integer LWORK = -1;
  46 + double WORK[1];
  47 + integer INFO;
  48 + dgetri_((integer*)&N, A, (integer*)&LDA, (integer*)IPIV, WORK, &LWORK, &INFO);
  49 +}
0 \ No newline at end of file 50 \ No newline at end of file
src/linalg.h 0 → 100644
  Show/Hide comments   View file @18c1cc4
  1 +void LINALG_dgeev(
  2 + char JOBVL,
  3 + char JOBVR,
  4 + int n,
  5 + double* A,
  6 + int LDA,
  7 + double* WR,
  8 + double* WI,
  9 + double* VL,
  10 + int LDVL,
  11 + double* VR,
  12 + int LDVR);
  13 +
  14 +void LINALG_dgetrf(
  15 + int M,
  16 + int N,
  17 + double* A,
  18 + int LDA,
  19 + int* IPIV);
  20 +
  21 +void LINALG_dgetri(
  22 + int N,
  23 + double* A,
  24 + int LDA,
  25 + int* IPIV);
0 \ No newline at end of file 26 \ No newline at end of file
src/proc/hsiproc.cpp
  Show/Hide comments   View file @18c1cc4
  1 +//#include "lapacke.h"
  2 +//#include "cblas.h"
  3 +
  4 +//#include <string>
  5 +#include "linalg.h"
  6 +
1 #include <iostream> 7 #include <iostream>
2 #include <fstream> 8 #include <fstream>
3 #include <random> 9 #include <random>
@@ -13,18 +19,16 @@ @@ -13,18 +19,16 @@
13 #include <stim/envi/agilent_binary.h> 19 #include <stim/envi/agilent_binary.h>
14 #include <stim/math/matrix.h> 20 #include <stim/math/matrix.h>
15 #include <time.h> 21 #include <time.h>
16 -#include <fstream>  
17 #include <thread> 22 #include <thread>
18 23
19 //LAPACKE support for Visual Studio 24 //LAPACKE support for Visual Studio
20 -#include <complex>  
21 -#ifndef LAPACK_COMPLEX_CUSTOM  
22 -#define LAPACK_COMPLEX_CUSTOM  
23 -#define lapack_complex_float std::complex<float>  
24 -#define lapack_complex_double std::complex<double>  
25 -#endif  
26 -#include "lapacke.h"  
27 -//#include "cblas.h" 25 +//#include <complex>
  26 +//#ifndef LAPACK_COMPLEX_CUSTOM
  27 +//#define LAPACK_COMPLEX_CUSTOM
  28 +//#define lapack_complex_float std::complex<float>
  29 +//#define lapack_complex_double std::complex<double>
  30 +//#endif
  31 +
28 32
29 void baseline(std::string infile, std::string outfile, std::string headerfile, std::vector<double> points, unsigned char* mask); 33 void baseline(std::string infile, std::string outfile, std::string headerfile, std::vector<double> points, unsigned char* mask);
30 void normalize(std::string infile, std::string outfile, std::string headerfile, double band, unsigned char* mask); 34 void normalize(std::string infile, std::string outfile, std::string headerfile, double band, unsigned char* mask);
@@ -512,12 +516,6 @@ int main(int argc, char** argv){ @@ -512,12 +516,6 @@ int main(int argc, char** argv){
512 //output the average spectrum 516 //output the average spectrum
513 std::ofstream csv(outfile.c_str()); //open a CSV file to write the mean 517 std::ofstream csv(outfile.c_str()); //open a CSV file to write the mean
514 518
515 - /*if (ENVI.header.wavelength.size() > 0) //output the first wavelength  
516 - csv << ENVI.header.wavelength[0]<<',';  
517 - csv << spectrum[0]; //output the first variable  
518 - for (unsigned long long b = 1; b < B; b++) //for each band  
519 - csv << "," << spectrum[b]; //output the next variable  
520 - */  
521 for (unsigned long long b = 0; b < B; b++) { //for each band 519 for (unsigned long long b = 0; b < B; b++) { //for each band
522 if (ENVI.header.wavelength.size() == B) //output the wavelength, if available 520 if (ENVI.header.wavelength.size() == B) //output the wavelength, if available
523 csv << ENVI.header.wavelength[b] << ','; 521 csv << ENVI.header.wavelength[b] << ',';
@@ -552,22 +550,6 @@ int main(int argc, char** argv){ @@ -552,22 +550,6 @@ int main(int argc, char** argv){
552 csv << m[b] << "," << std[b] << std::endl; 550 csv << m[b] << "," << std[b] << std::endl;
553 } 551 }
554 552
555 -  
556 -  
557 -  
558 -  
559 - //output the average spectrum  
560 - /*std::ofstream csv(outfile.c_str()); //open a CSV file to write the mean  
561 - csv<<m[0]; //output the first variable  
562 - for(unsigned long long b = 1; b < B; b++) //for each band  
563 - csv<<","<<m[b]; //output the next variable  
564 -  
565 - //output the standard deviation  
566 - csv<<std::endl;  
567 - csv<<std[0];  
568 - for(unsigned long long b = 1; b < B; b++) //for each band  
569 - csv<<","<<std[b]; //output the next variable  
570 - */  
571 csv.close(); //close the output file 553 csv.close(); //close the output file
572 554
573 free(m); //free memory storing the mean spectrum 555 free(m); //free memory storing the mean spectrum
@@ -703,9 +685,13 @@ int main(int argc, char** argv){ @@ -703,9 +685,13 @@ int main(int argc, char** argv){
703 685
704 stim::matrix<double> JtJi = JtJ; //allocate space for the matrix inverse 686 stim::matrix<double> JtJi = JtJ; //allocate space for the matrix inverse
705 int* piv = (int*) malloc(JtJi.rows() * sizeof(int)); //allocate space to store the LU decomposition pivot indices 687 int* piv = (int*) malloc(JtJi.rows() * sizeof(int)); //allocate space to store the LU decomposition pivot indices
706 - LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)JtJi.rows(), (int)JtJi.cols(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK for LU decomposition  
707 - LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)JtJi.rows(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK to solve the inverse 688 + //LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)JtJi.rows(), (int)JtJi.cols(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK for LU decomposition
  689 + //LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)JtJi.rows(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK to solve the inverse
708 690
  691 + // REPLACED THE ABOVE LAPACKE functions with new CLAPACK functions in linalg.cpp
  692 + LINALG_dgetrf((int)JtJi.rows(), (int)JtJi.cols(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK for LU decomposition
  693 + LINALG_dgetri((int)JtJi.rows(), JtJi.data(), (int)JtJi.rows(), piv); //use LAPACK to solve the inverse
  694 +
709 695
710 stim::matrix<double> C = JtJi * Jt; //calculate C 696 stim::matrix<double> C = JtJi * Jt; //calculate C
711 697
@@ -781,7 +767,12 @@ int main(int argc, char** argv){ @@ -781,7 +767,12 @@ int main(int argc, char** argv){
781 double* lambda_real = (double*) malloc(B * sizeof(double)); 767 double* lambda_real = (double*) malloc(B * sizeof(double));
782 double* lambda_imag = (double*) malloc(B * sizeof(double)); 768 double* lambda_imag = (double*) malloc(B * sizeof(double));
783 double* evec = (double*) malloc(B * B * sizeof(double)); 769 double* evec = (double*) malloc(B * B * sizeof(double));
784 - LAPACKE_dgeev(LAPACK_COL_MAJOR, 'N', 'V', (int)B, co, (int)B, lambda_real, lambda_imag, NULL, (int)B, evec, (int)B); 770 + //LAPACKE_dgeev(LAPACK_COL_MAJOR, 'N', 'V', (int)B, co, (int)B, lambda_real, lambda_imag, NULL, (int)B, evec, (int)B);
  771 +
  772 + // REPLACED THE ABOVE LAPACKE functions with new CLAPACK functions in linalg.cpp
  773 + LINALG_dgeev('N', 'V', (int)B, co, (int)B, lambda_real, lambda_imag, NULL, (int)B, evec, (int)B);
  774 +
  775 +
785 std::ofstream csv(outfile.c_str(), std::ios::out); //create a text file to store the PCA stats (mean and covariance matrix) 776 std::ofstream csv(outfile.c_str(), std::ios::out); //create a text file to store the PCA stats (mean and covariance matrix)
786 777
787 csv<<mu[0]; //output the mean spectrum 778 csv<<mu[0]; //output the mean spectrum
@@ -789,12 +780,6 @@ int main(int argc, char** argv){ @@ -789,12 +780,6 @@ int main(int argc, char** argv){
789 csv<<","<<mu[i]; 780 csv<<","<<mu[i];
790 csv<<std::endl; 781 csv<<std::endl;
791 782
792 - /*for (unsigned long long j = 0; j < B; j++){ //output the principle components  
793 - csv<<eigenvectors.at<double>((int)j, 0);  
794 - for (unsigned long long i = 1; i < B; i++)  
795 - csv<<","<<eigenvectors.at<double>((int)j, (int)i);  
796 - csv << std::endl;  
797 - }*/  
798 for(size_t j = 0; j < B; j++){ 783 for(size_t j = 0; j < B; j++){
799 csv<<evec[j * B + 0]; //output the first element of the eigenvector 784 csv<<evec[j * B + 0]; //output the first element of the eigenvector
800 for(size_t i = 1; i < B; i++){ 785 for(size_t i = 1; i < B; i++){
@@ -1060,85 +1045,7 @@ int main(int argc, char** argv){ @@ -1060,85 +1045,7 @@ int main(int argc, char** argv){
1060 t1.join(); //wait for the progress bar thread to finish (it probably already is) 1045 t1.join(); //wait for the progress bar thread to finish (it probably already is)
1061 C.close(); //close the appended file 1046 C.close(); //close the appended file
1062 } 1047 }
1063 - /*else if(args["mosaic"].is_set()){  
1064 - if (args["mosaic"].as_string() == "cary"){  
1065 - //use the file extension to determine if the mosaic is an interferogram or spectrum  
1066 - stim::filename f(infile);  
1067 - if(f.extension() == "drd" || f.extension() == "DRD")  
1068 - mosaic_agilent_interferogram(infile, outfile, args["elwn"].as_float(0), args["udr"].as_int(0));  
1069 -  
1070 - }  
1071 - if(args["mosaic"].as_string(0) == "spero"){  
1072 - mosaic_spero(infile, outfile);  
1073 - }  
1074 - else {  
1075 - std::cout << "ERROR: mosaic construction has been moved to other executables." << std::endl;  
1076 - exit(1);  
1077 - }  
1078 - }*/  
1079 - /*else if(args["fft"].is_set()){ //if the user requests batch FFT processing  
1080 -  
1081 - double wn_min = args["fft-range"].as_float(0); //get the minimum and maximum bounds for the spectrum  
1082 - double wn_max = args["fft-range"].as_float(1);  
1083 - double elwn = args["elwn"].as_float(0); //get the Effective Laser Wave Number  
1084 - int udr = args["udr"].as_int(0); //get the UDR filter/sampling method  
1085 -  
1086 - bool ratio = false; //default to calculating a ratio  
1087 - void* background = NULL;  
1088 - stim::agilent_binary<float> bkg;  
1089 - if(args["background"].is_set()){ //if a background is specified  
1090 - stim::filename bkg_file(args["background"].as_string(0)); //create a filename for the background file  
1091 - if(bkg_file.extension() != "seq"){  
1092 - std::cout<<"ERROR - Agilent SEQ file expected for the background."<<std::endl;  
1093 - exit(1);  
1094 - }  
1095 - std::cout<<"background file: "<<args["background"].as_string(0)<<std::endl;  
1096 - bkg.load(args["background"].as_string(0)); //load the background interferogram  
1097 - ratio = true;  
1098 - }  
1099 - if(ENVI){ //if the input file is an ENVI mosaic  
1100 - std::thread t1(progress_thread_envi, &ENVI); //start the progress bar thread  
1101 -  
1102 - if(ratio){  
1103 - background = (void*) malloc(bkg.bytes()); //allocate a pointer for the raw background data  
1104 - bkg.bip((float*)background); //copy the background interferogram to a BIP file  
1105 - }  
1106 - size_t samples = 0;  
1107 - if(args["fft"].nargs() == 1) samples = args["fft"].as_int(0);  
1108 - ENVI.fft(outfile, wn_min, wn_max, samples, background, bkg.dim(0), bkg.dim(1), true, args["cuda"].as_int()); //if the input is an ENVI file, run the ENVI FFT  
1109 -  
1110 - t1.join(); //wait for the progress bar thread to finish (it probably already is)  
1111 - }*/  
1112 - /*else{  
1113 - stim::filepath fp = infile;  
1114 - stim::filename f(fp, "*.drd");  
1115 - std::vector<stim::filename> drd_list = f.get_list(); //generate a list of DRD files  
1116 - if(drd_list.size() == 0){  
1117 - std::cerr<<"ERROR: no interferogram (*.drd) files found."<<std::endl;  
1118 - exit(1);  
1119 - }  
1120 -  
1121 - double progress = 0;  
1122 - std::thread t1(progress_thread_double, &progress); //start the progress bar thread  
1123 - for(size_t i = 0; i < drd_list.size(); i++){  
1124 - //std::cout<<drd_list[i].str()<<std::endl;  
1125 - stim::agilent_binary<float> interferogram(drd_list[i].str()); //load the interferogram  
1126 - interferogram.meancenter(); //mean center the interferogram  
1127 - interferogram.zeropad(); //pad to the nearest power-of-two  
1128 - stim::agilent_binary<float> fft = interferogram.fft(wn_min, wn_max, elwn, udr); //calculate the FFT and crop out the desired wavenumber range  
1129 - if(i == 0){ //if this is the first file  
1130 - stim::envi_header header = fft.create_header(); //create a header  
1131 - header.save(drd_list[0].extension("hdr")); //save the header  
1132 - }  
1133 -  
1134 - if(ratio) fft.absorbance(&bkg_fft); //if we are calculating a ratio to a background, calculate the absorbance  
1135 - fft.save(drd_list[i].extension("dmd")); //save the output file as a DMD  
1136 - //std::cout<<progress<<std::endl;  
1137 - progress = (double)(i+1) / (double) drd_list.size() * 100;  
1138 - }  
1139 - t1.join(); //wait for the progress bar thread to finish (it probably already is)  
1140 - }  
1141 - }*/ 1048 +
1142 else if(args["mnf"].is_set()){ 1049 else if(args["mnf"].is_set()){
1143 if (args["mnf"].nargs() == 0){ 1050 if (args["mnf"].nargs() == 0){
1144 std::cout << "ERROR: no mnf parameters specified" << std::endl; 1051 std::cout << "ERROR: no mnf parameters specified" << std::endl;
@@ -1176,4 +1083,4 @@ int main(int argc, char** argv){ @@ -1176,4 +1083,4 @@ int main(int argc, char** argv){
1176 1083
1177 //close the input file 1084 //close the input file
1178 ENVI.close(); 1085 ENVI.close();
1179 -} 1086 -}
  1087 +}
1180 \ No newline at end of file 1088 \ No newline at end of file
  1 +#include "linalg.h"
  2 +
1 #include <iostream> 3 #include <iostream>
2 #include <stim/envi/envi.h> 4 #include <stim/envi/envi.h>
3 #include "stim/envi/envi_header.h" 5 #include "stim/envi/envi_header.h"
@@ -5,20 +7,18 @@ @@ -5,20 +7,18 @@
5 #include <stim/image/image.h> 7 #include <stim/image/image.h>
6 #include <stim/math/matrix.h> 8 #include <stim/math/matrix.h>
7 #include <time.h> 9 #include <time.h>
8 -//#include <opencv2/opencv.hpp>  
9 #include <fstream> 10 #include <fstream>
10 #include <thread> 11 #include <thread>
11 #include "stim/envi/bil.h" 12 #include "stim/envi/bil.h"
12 -//#include <opencv2/core/core.hpp>  
13 13
14 //LAPACKE support for Visual Studio 14 //LAPACKE support for Visual Studio
15 -#include <complex>  
16 -#ifndef LAPACK_COMPLEX_CUSTOM  
17 -#define LAPACK_COMPLEX_CUSTOM  
18 -#define lapack_complex_float std::complex<float>  
19 -#define lapack_complex_double std::complex<double>  
20 -#endif  
21 -#include "lapacke.h" 15 +//#include <complex>
  16 +//#ifndef LAPACK_COMPLEX_CUSTOM
  17 +//#define LAPACK_COMPLEX_CUSTOM
  18 +//#define lapack_complex_float std::complex<float>
  19 +//#define lapack_complex_double std::complex<double>
  20 +//#endif
  21 +//#include "lapacke.h"
22 22
23 23
24 24
@@ -101,8 +101,14 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in @@ -101,8 +101,14 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in
101 101
102 std::cout << std::endl << "Calculating the inverse covariance matrix S^(-1)..."; 102 std::cout << std::endl << "Calculating the inverse covariance matrix S^(-1)...";
103 int *IPIV = (int*)malloc(sizeof(int) * B); 103 int *IPIV = (int*)malloc(sizeof(int) * B);
104 - LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)B, (int)B, cov.data(), (int)B, IPIV); //perform LU factorization  
105 - LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)B, cov.data(), (int)B, IPIV); //calculate matrix inverse 104 +
  105 + //LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)B, (int)B, cov.data(), (int)B, IPIV); //perform LU factorization
  106 + //LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)B, cov.data(), (int)B, IPIV); //calculate matrix inverse
  107 +
  108 + // REPLACED THE ABOVE LAPACKE functions with new CLAPACK functions in linalg.cpp
  109 + LINALG_dgetrf((int)B, (int)B, cov.data(), (int)B, IPIV); //perform LU factorization
  110 + LINALG_dgetri((int)B, cov.data(), (int)B, IPIV); //calculate matrix inverse
  111 +
106 free(IPIV); 112 free(IPIV);
107 std::cout << "done." << std::endl; 113 std::cout << "done." << std::endl;
108 114
@@ -118,7 +124,11 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in @@ -118,7 +124,11 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in
118 124
119 std::cout << std::endl << "Calculating left eigenvectors X * A = v * X..."; 125 std::cout << std::endl << "Calculating left eigenvectors X * A = v * X...";
120 stim::matrix<double> ev_left(B, B); 126 stim::matrix<double> ev_left(B, B);
121 - LAPACKE_dgeev(LAPACK_COL_MAJOR, 'V', 'N', (int)B, Q.data(), (int)B, EigenvaluesReal, EigenvaluesIm, ev_left.data(), (int)B, 0, (int)B); //perform eigenvalue decomposition 127 + //LAPACKE_dgeev(LAPACK_COL_MAJOR, 'V', 'N', (int)B, Q.data(), (int)B, EigenvaluesReal, EigenvaluesIm, ev_left.data(), (int)B, 0, (int)B); //perform eigenvalue decomposition
  128 +
  129 + // REPLACED THE ABOVE LAPACKE functions with new CLAPACK functions in linalg.cpp
  130 + LINALG_dgeev('V', 'N', (int)B, Q.data(), (int)B, EigenvaluesReal, EigenvaluesIm, ev_left.data(), (int)B, 0, (int)B); //perform eigenvalue decomposition
  131 +
122 std::cout << "done." << std::endl; 132 std::cout << "done." << std::endl;
123 133
124 std::cout << std::endl << "Sorting eigenvectors..."; 134 std::cout << std::endl << "Sorting eigenvectors...";
@@ -157,8 +167,13 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in @@ -157,8 +167,13 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in
157 167
158 //calculate inverse of As matrix 168 //calculate inverse of As matrix
159 int *IPIV2 = (int*)malloc(sizeof(int) * B); 169 int *IPIV2 = (int*)malloc(sizeof(int) * B);
160 - LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)B, (int)B, As.data(), (int)B, IPIV2);  
161 - LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)B, As.data(), (int)B, IPIV2); 170 + //LAPACKE_dgetrf(LAPACK_COL_MAJOR, (int)B, (int)B, As.data(), (int)B, IPIV2);
  171 + //LAPACKE_dgetri(LAPACK_COL_MAJOR, (int)B, As.data(), (int)B, IPIV2);
  172 +
  173 + // REPLACED THE ABOVE LAPACKE functions with new CLAPACK functions in linalg.cpp
  174 + LINALG_dgetrf((int)B, (int)B, As.data(), (int)B, IPIV2);
  175 + LINALG_dgetri((int)B, As.data(), (int)B, IPIV2);
  176 +
162 free(IPIV2); 177 free(IPIV2);
163 178
164 //calculate transpose of As inversed matrix (transpose of transformation matrix inveresed ) . 179 //calculate transpose of As inversed matrix (transpose of transformation matrix inveresed ) .
@@ -186,4 +201,4 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in @@ -186,4 +201,4 @@ void mnf(std::string outfile, int keptComponents, std::string NoiseFractions, in
186 csv << "\n" << EigenSortedIndices[b] << ", " << EigenvaluesReal[EigenSortedIndices[b]]; //output the next variable 201 csv << "\n" << EigenSortedIndices[b] << ", " << EigenvaluesReal[EigenSortedIndices[b]]; //output the next variable
187 csv.close(); 202 csv.close();
188 } 203 }
189 -} //end MNF 204 -} //end MNF
  205 +} //end MNF
190 \ No newline at end of file 206 \ No newline at end of file