codebase / stimlib

Commit 29165fa9f11d4dfef9775edef9d4fcab9f174644

Authored by David Mayerich
1 parent 35a7195f

added ROC curve calculations and padding to agilent_binary

Showing 6 changed files with 463 additions and 4 deletions   Show diff stats
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cmake/FindFANN.cmake 0 → 100644
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  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 fann doublefann fixedfann 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 +
  46 + endforeach()
  47 +
  48 +
  49 + set(FANN_INCLUDE_DIRS
  50 + ${FANN_INCLUDE_DIR}
  51 + )
  52 +
  53 + set(FANN_LIBRARIES
  54 + ${FANN_LIBRARIES}
  55 + ${FANN_LIBRARY}
  56 + ${DOUBLEFANN_LIBRARY}
  57 + ${FIXEDFANN_LIBRARY}
  58 + ${FLOATFANN_LIBRARY}
  59 + )
  60 +
  61 + if( UNIX )
  62 + set( FANN_LIBRARIES ${FANN_LIBRARIES} m )
  63 + endif()
  64 +
  65 + if(FANN_INCLUDE_DIRS AND FANN_LIBRARIES)
  66 + set(FANN_FOUND TRUE)
  67 + endif()
  68 +
  69 + if(FANN_FOUND)
  70 + if(NOT FANN_FIND_QUIETLY)
  71 + message(STATUS "Found FANN:")
  72 + message(STATUS "FANN_INCLUDE_DIRS: ${FANN_INCLUDE_DIRS}")
  73 + message(STATUS "FANN_LIBRARIES: ${FANN_LIBRARIES}")
  74 + endif()
  75 + else()
  76 + if(FANN_FIND_REQUIRED)
  77 + message(FATAL_ERROR "Could not find FANN")
  78 + endif()
  79 + endif()
  80 +
  81 + mark_as_advanced(FANN_INCLUDE_DIRS FANN_LIBRARIES)
  82 +endif()
... ...
cmake/FindGLEW.cmake 0 → 100644
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  1 +#
  2 +# Windows users: define the GLEW_PATH environment variable to point
  3 +# to the root glew directory, which contains:
  4 +# lib/Release/Win32/glew32.lib AND/OR lib/Release/x64/glew32.lib
  5 +# include/GL/glew.h
  6 +
  7 +#Try to find GLEW library and include path.
  8 +# Once done this will define
  9 +#
  10 +# GLEW_FOUND
  11 +# GLEW_INCLUDE_DIR
  12 +# GLEW_LIBRARY
  13 +#
  14 +
  15 +IF (WIN32)
  16 + FIND_PATH( GLEW_INCLUDE_DIR GL/glew.h
  17 + $ENV{GLEW_PATH}/include
  18 + $ENV{PROGRAMFILES}/GLEW/include
  19 + ${PROJECT_SOURCE_DIR}/src/nvgl/glew/include
  20 + DOC "The directory where GL/glew.h resides")
  21 + if( CMAKE_SIZEOF_VOID_P EQUAL 8 )
  22 + FIND_LIBRARY( GLEW_LIBRARY
  23 + NAMES glew GLEW glew32 glew32s
  24 + PATHS
  25 + $ENV{GLEW_PATH}/lib/Release/x64
  26 + $ENV{PROGRAMFILES}/GLEW/lib
  27 + ${PROJECT_SOURCE_DIR}/src/nvgl/glew/bin
  28 + ${PROJECT_SOURCE_DIR}/src/nvgl/glew/lib
  29 + DOC "The GLEW library")
  30 + else( CMAKE_SIZEOF_VOID_P EQUAL 8 )
  31 + FIND_LIBRARY( GLEW_LIBRARY
  32 + NAMES glew GLEW glew32 glew32s
  33 + PATHS
  34 + $ENV{GLEW_PATH}/lib/Release/Win32
  35 + $ENV{PROGRAMFILES}/GLEW/lib
  36 + ${PROJECT_SOURCE_DIR}/src/nvgl/glew/bin
  37 + ${PROJECT_SOURCE_DIR}/src/nvgl/glew/lib
  38 + DOC "The GLEW library")
  39 + endif( CMAKE_SIZEOF_VOID_P EQUAL 8 )
  40 +ELSE (WIN32)
  41 + FIND_PATH( GLEW_INCLUDE_DIR GL/glew.h
  42 + /usr/include
  43 + /usr/local/include
  44 + /sw/include
  45 + /opt/local/include
  46 + DOC "The directory where GL/glew.h resides")
  47 + FIND_LIBRARY( GLEW_LIBRARY
  48 + NAMES GLEW glew
  49 + PATHS
  50 + /usr/lib64
  51 + /usr/lib
  52 + /usr/local/lib64
  53 + /usr/local/lib
  54 + /sw/lib
  55 + /opt/local/lib
  56 + DOC "The GLEW library")
  57 +ENDIF (WIN32)
  58 +
  59 +IF (GLEW_INCLUDE_DIR)
  60 + SET( GLEW_FOUND 1 CACHE STRING "Set to 1 if GLEW is found, 0 otherwise")
  61 +ELSE (GLEW_INCLUDE_DIR)
  62 + SET( GLEW_FOUND 0 CACHE STRING "Set to 1 if GLEW is found, 0 otherwise")
  63 +ENDIF (GLEW_INCLUDE_DIR)
  64 +
  65 +MARK_AS_ADVANCED(
  66 + GLEW_FOUND
  67 + GLEW_INCLUDE_DIR
  68 + GLEW_LIBRARY
  69 +)
0 70 \ No newline at end of file
... ...
cmake/FindGLUT.cmake 0 → 100644
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  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_PATH}/include )
  50 +
  51 + if( CMAKE_SIZEOF_VOID_P EQUAL 8 )
  52 + find_library( GLUT_glut_LIBRARY NAMES freeglut
  53 + PATHS
  54 + $ENV{GLUT_ROOT_PATH}/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 + ${OPENGL_LIBRARY_DIR}
  62 + $ENV{GLUT_ROOT_PATH}/lib
  63 + )
  64 + endif( CMAKE_SIZEOF_VOID_P EQUAL 8 )
  65 +
  66 +else ()
  67 +
  68 + if (APPLE)
  69 + find_path(GLUT_INCLUDE_DIR glut.h ${OPENGL_LIBRARY_DIR})
  70 + find_library(GLUT_glut_LIBRARY GLUT DOC "GLUT library for OSX")
  71 + find_library(GLUT_cocoa_LIBRARY Cocoa DOC "Cocoa framework for OSX")
  72 +
  73 + if(GLUT_cocoa_LIBRARY AND NOT TARGET GLUT::Cocoa)
  74 + add_library(GLUT::Cocoa UNKNOWN IMPORTED)
  75 + # Cocoa should always be a Framework, but we check to make sure.
  76 + if(GLUT_cocoa_LIBRARY MATCHES "/([^/]+)\\.framework$")
  77 + set_target_properties(GLUT::Cocoa PROPERTIES
  78 + IMPORTED_LOCATION "${GLUT_cocoa_LIBRARY}/${CMAKE_MATCH_1}")
  79 + else()
  80 + set_target_properties(GLUT::Cocoa PROPERTIES
  81 + IMPORTED_LOCATION "${GLUT_cocoa_LIBRARY}")
  82 + endif()
  83 + endif()
  84 + else ()
  85 +
  86 + if (BEOS)
  87 +
  88 + set(_GLUT_INC_DIR /boot/develop/headers/os/opengl)
  89 + set(_GLUT_glut_LIB_DIR /boot/develop/lib/x86)
  90 +
  91 + else()
  92 +
  93 + find_library( GLUT_Xi_LIBRARY Xi
  94 + /usr/openwin/lib
  95 + )
  96 +
  97 + find_library( GLUT_Xmu_LIBRARY Xmu
  98 + /usr/openwin/lib
  99 + )
  100 +
  101 + if(GLUT_Xi_LIBRARY AND NOT TARGET GLUT::Xi)
  102 + add_library(GLUT::Xi UNKNOWN IMPORTED)
  103 + set_target_properties(GLUT::Xi PROPERTIES
  104 + IMPORTED_LOCATION "${GLUT_Xi_LIBRARY}")
  105 + endif()
  106 +
  107 + if(GLUT_Xmu_LIBRARY AND NOT TARGET GLUT::Xmu)
  108 + add_library(GLUT::Xmu UNKNOWN IMPORTED)
  109 + set_target_properties(GLUT::Xmu PROPERTIES
  110 + IMPORTED_LOCATION "${GLUT_Xmu_LIBRARY}")
  111 + endif()
  112 +
  113 + endif ()
  114 +
  115 + find_path( GLUT_INCLUDE_DIR GL/glut.h
  116 + /usr/include/GL
  117 + /usr/openwin/share/include
  118 + /usr/openwin/include
  119 + /opt/graphics/OpenGL/include
  120 + /opt/graphics/OpenGL/contrib/libglut
  121 + ${_GLUT_INC_DIR}
  122 + )
  123 +
  124 + find_library( GLUT_glut_LIBRARY glut
  125 + /usr/openwin/lib
  126 + ${_GLUT_glut_LIB_DIR}
  127 + )
  128 +
  129 + unset(_GLUT_INC_DIR)
  130 + unset(_GLUT_glut_LIB_DIR)
  131 +
  132 + endif ()
  133 +
  134 +endif ()
  135 +
  136 +FIND_PACKAGE_HANDLE_STANDARD_ARGS(GLUT REQUIRED_VARS GLUT_glut_LIBRARY GLUT_INCLUDE_DIR)
  137 +
  138 +if (GLUT_FOUND)
  139 + # Is -lXi and -lXmu required on all platforms that have it?
  140 + # If not, we need some way to figure out what platform we are on.
  141 + set( GLUT_LIBRARIES
  142 + ${GLUT_glut_LIBRARY}
  143 + ${GLUT_Xmu_LIBRARY}
  144 + ${GLUT_Xi_LIBRARY}
  145 + ${GLUT_cocoa_LIBRARY}
  146 + )
  147 +
  148 + if(NOT TARGET GLUT::GLUT)
  149 + add_library(GLUT::GLUT UNKNOWN IMPORTED)
  150 + set_target_properties(GLUT::GLUT PROPERTIES
  151 + INTERFACE_INCLUDE_DIRECTORIES "${GLUT_INCLUDE_DIR}")
  152 + if(GLUT_glut_LIBRARY MATCHES "/([^/]+)\\.framework$")
  153 + set_target_properties(GLUT::GLUT PROPERTIES
  154 + IMPORTED_LOCATION "${GLUT_glut_LIBRARY}/${CMAKE_MATCH_1}")
  155 + else()
  156 + set_target_properties(GLUT::GLUT PROPERTIES
  157 + IMPORTED_LOCATION "${GLUT_glut_LIBRARY}")
  158 + endif()
  159 +
  160 + if(TARGET GLUT::Xmu)
  161 + set_property(TARGET GLUT::GLUT APPEND
  162 + PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Xmu)
  163 + endif()
  164 +
  165 + if(TARGET GLUT::Xi)
  166 + set_property(TARGET GLUT::GLUT APPEND
  167 + PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Xi)
  168 + endif()
  169 +
  170 + if(TARGET GLUT::Cocoa)
  171 + set_property(TARGET GLUT::GLUT APPEND
  172 + PROPERTY INTERFACE_LINK_LIBRARIES GLUT::Cocoa)
  173 + endif()
  174 + endif()
  175 +
  176 + #The following deprecated settings are for backwards compatibility with CMake1.4
  177 + set (GLUT_LIBRARY ${GLUT_LIBRARIES})
  178 + set (GLUT_INCLUDE_PATH ${GLUT_INCLUDE_DIR})
  179 +endif()
  180 +
  181 +mark_as_advanced(
  182 + GLUT_INCLUDE_DIR
  183 + GLUT_glut_LIBRARY
  184 + GLUT_Xmu_LIBRARY
  185 + GLUT_Xi_LIBRARY
  186 + )
... ...
matlab/stimLoadAgilent.m 0 → 100644
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  1 +%Loads a standard Agilent ResPro binary file
  2 +% stimLoadAgilent(filename)
  3 +function S = stimLoadAgilent(filename)
  4 +
  5 + fid = fopen(filename);
  6 + fseek(fid, 9, 'bof');
  7 + Z = fread(fid, 1, 'uint16');
  8 + fseek(fid, 13, 'cof');
  9 + X = fread(fid, 1, 'uint16');
  10 + Y = fread(fid, 1, 'uint16');
  11 +
  12 + fseek(fid, 1020, 'bof');
  13 +
  14 + S = reshape(fread(fid, [X, Y * Z], 'float32'), [X, Y, Z]);
  15 +
  16 +
0 17 \ No newline at end of file
... ...
matlab/stimROC.m 0 → 100644
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  1 +function [TPR, FPR, AUC] = stimROC(C, T)
  2 +%build an ROC curve
  3 +% C - class labels as an array of binary values (1 = true positive)
  4 +% T - threshold used for classification
  5 +
  6 + %sort the thresholds in descending order and get the indices
  7 + [~, I] = sort(T, 'descend');
  8 +
  9 + %sort the class labels in the same order as the thresholds
  10 + Cs = C(I);
  11 +
  12 + %calculate the number of measurements
  13 + M = size(C, 2);
  14 +
  15 + %calculate the number of positives
  16 + P = nnz(C);
  17 +
  18 + %calculate the number of negatives
  19 + N = M - P;
  20 +
  21 + %if all examples are positives or negatives, return a perfect score?
  22 + if P == M
  23 + error('ERROR: no positive observations');
  24 + end
  25 + if P == 0
  26 + error('ERROR: no negative observations');
  27 + end
  28 +
  29 + %allocate space for the ROC curve
  30 + TPR = zeros(1, M);
  31 + FPR = zeros(1, M);
  32 +
  33 +
  34 +
  35 + %calculate the number of inflection points
  36 + ip = 0;
  37 + for i = 2:M
  38 + if Cs(i) ~= Cs(i-1)
  39 + ip = ip + 1;
  40 + end
  41 + end
  42 +
  43 + %initialize the true and false positive rates to zero
  44 + TP = 0;
  45 + FP = 0;
  46 + for i = 1:M
  47 + if Cs(i) == 1
  48 + TP = TP + 1;
  49 + else
  50 + FP = FP + 1;
  51 + end
  52 +
  53 + TPR(i) = TP / P;
  54 + FPR(i) = FP / N;
  55 + end
  56 +
  57 + %calculate the area under the ROC curve
  58 + AUC = 0;
  59 + for i = 2:M
  60 + w = FPR(i) - FPR(i-1);
  61 + h = TPR(i);
  62 + AUC = AUC + w * h;
  63 + end
  64 +
  65 +
  66 +
  67 +
  68 +
  69 +
0 70 \ No newline at end of file
... ...
stim/envi/agilent_binary.h
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... ... @@ -19,10 +19,10 @@ class agilent_binary{
19 19  
20 20 protected:
21 21 std::string fname;
22   - T* ptr;
23   - size_t R[3];
24   - static const size_t header = 1020;
25   - double Z[2];
  22 + T* ptr; //pointer to the image data
  23 + size_t R[3]; //size of the binary image in X, Y, and Z
  24 + static const size_t header = 1020; //header size
  25 + double Z[2]; //range of z values (position or wavelength)
26 26  
27 27 public:
28 28 size_t size(){
... ... @@ -136,6 +136,43 @@ public:
136 136 return header;
137 137 }
138 138  
  139 + /// Subtract the mean from each pixel. Generally used for centering an interferogram.
  140 + void meancenter(){
  141 + size_t Z = R[2]; //store the number of bands
  142 + size_t XY = R[0] * R[1]; //store the number of pixels in the image
  143 + T sum = (T)0;
  144 + T mean;
  145 + for(size_t xy = 0; xy < XY; xy++){ //for each pixel
  146 + sum = 0;
  147 + for(size_t z = 0; z < Z; z++){ //for each band
  148 + sum += ptr[ z * XY + xy ]; //add the band value to a running sum
  149 + }
  150 + mean = sum / (T)Z; //calculate the pixel mean
  151 + for(size_t z = 0; z < Z; z++){
  152 + ptr[ z * XY + xy ] -= mean; //subtract the mean from each band
  153 + }
  154 + }
  155 + }
  156 +
  157 + /// adds n bands of zero padding to the end of the file
  158 + void zeropad(size_t n){
  159 + size_t newZ = R[2] + n;
  160 + T* temp = (T*) calloc(R[0] * R[1] * newZ, sizeof(T)); //allocate space for the new image
  161 + memcpy(temp, ptr, size() * sizeof(T)); //copy the old data to the new image
  162 +
  163 + free(ptr); //free the old data
  164 + ptr = temp; //swap in the new data
  165 + R[2] = newZ; //set the z-dimension to the new zero value
  166 + }
  167 +
  168 + //pads to the nearest power-of-two
  169 + void zeropad(){
  170 + size_t newZ = pow(2, ceil(log(R[2])/log(2))); //find the nearest power-of-two
  171 + size_t n = newZ - R[2]; //calculate the number of bands to add
  172 + std::cout<<"band padding: "<<n<<std::endl;
  173 + zeropad(n); //add the padding
  174 + }
  175 +
139 176 /// Calculate the absorbance spectrum from the transmission spectrum given a background
140 177 void absorbance(stim::agilent_binary<T>* background){
141 178 size_t N = size(); //calculate the number of values to be ratioed
... ...