segmentation / netmets

Commit a0048e3147823a5e3b76965870a8e8f1d0672ca7

Authored by David Mayerich
1 parent 03c5492b

added several test cases, implemented a simple test of loading networks from OBJ files

Showing 14 changed files with 210 additions and 48 deletions   Show diff stats
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CMakeLists.txt
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... ... @@ -7,9 +7,6 @@ project(netMets)
7 7 #set the module directory
8 8 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
9 9  
10   -#set up CUDA
11   -find_package(CUDA REQUIRED)
12   -
13 10 #find the STIM library
14 11 find_package(STIM REQUIRED)
15 12  
... ... @@ -22,36 +19,46 @@ find_package(Threads)
22 19 #find the X11 package
23 20 find_package(X11)
24 21  
25   -
26 22 #find the Approximate Nearest Neighbor Library
27 23 find_package(ANN REQUIRED)
28 24  
  25 +if ( MSVC )
  26 + SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG "${OUTPUT_DIRECTORY}")
  27 + SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE "${OUTPUT_DIRECTORY}")
  28 +endif ( MSVC )
  29 +
29 30 include_directories(
30 31 ${STIM_INCLUDE_DIRS}
31   - ${ANN_INCLUDE_DIR}
  32 + ${ANN_INCLUDE_DIR}
32 33 ${Boost_INCLUDE_DIR}
33 34 )
34 35  
35 36 #Assign source files to the appropriate variables
36 37 file(GLOB SRC_CPP "*.cpp")
37 38 file(GLOB SRC_H "*.h")
38   -file(GLOB SRC_CU "*.cu")
39   -file(GLOB SRC_CUH "*.cuh")
40 39  
41 40 #create an executable file
42   -cuda_add_executable(netmets
43   - ${SRC_H}
44   - ${SRC_CPP}
45   - ${SRC_CU}
46   - ${SRC_CUH}
  41 +add_executable(netmets
  42 + ${SRC_H}
  43 + ${SRC_CPP}
47 44 )
48 45  
49 46 #set the link libraries
50 47 target_link_libraries(netmets
51   - #${CUDA_cufft_LIBRARY}
52   - #${CUDA_cublas_LIBRARY}
53 48 ${CMAKE_THREAD_LIBS_INIT}
54   - ${ANN_LIBRARY}
  49 + ${ANN_LIBRARY}
55 50 ${X11_LIBRARIES}
56 51 )
57 52  
  53 +#set up copying data files
  54 +configure_file(data/00_GT.obj ${CMAKE_CURRENT_BINARY_DIR}/00_GT.obj @ONLY)
  55 +configure_file(data/00_T.obj ${CMAKE_CURRENT_BINARY_DIR}/00_T.obj @ONLY)
  56 +configure_file(data/01_GT.obj ${CMAKE_CURRENT_BINARY_DIR}/01_GT.obj @ONLY)
  57 +configure_file(data/01_T.obj ${CMAKE_CURRENT_BINARY_DIR}/01_T.obj @ONLY)
  58 +configure_file(data/02_GT.obj ${CMAKE_CURRENT_BINARY_DIR}/02_GT.obj @ONLY)
  59 +configure_file(data/02_T.obj ${CMAKE_CURRENT_BINARY_DIR}/02_T.obj @ONLY)
  60 +configure_file(data/03_GT.obj ${CMAKE_CURRENT_BINARY_DIR}/03_GT.obj @ONLY)
  61 +configure_file(data/03_T.obj ${CMAKE_CURRENT_BINARY_DIR}/03_T.obj @ONLY)
  62 +configure_file(data/04_GT.obj ${CMAKE_CURRENT_BINARY_DIR}/04_GT.obj @ONLY)
  63 +configure_file(data/04_Ta.obj ${CMAKE_CURRENT_BINARY_DIR}/04_Ta.obj @ONLY)
  64 +configure_file(data/04_Tb.obj ${CMAKE_CURRENT_BINARY_DIR}/04_Tb.obj @ONLY)
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00_T.obj renamed to data/00_T.obj
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main.cpp
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... ... @@ -2,7 +2,7 @@
2 2 #include <string>
3 3 #include <fstream>
4 4 #include <algorithm>
5   -#include <stim/visualization/network.h>
  5 +#include <stim/biomodels/network.h>
6 6  
7 7 #include <ANN/ANN.h>
8 8 #include <boost/tuple/tuple.hpp>
... ... @@ -13,15 +13,29 @@ network&lt;float&gt;* network1;
13 13  
14 14 int main(int argc, char* argv[])
15 15 {
16   - std::string groundTruth = argv[1];
  16 + if(argc < 4){
  17 + std::cout<<"Please specify a ground truth and test case"<<std::endl;
  18 + exit(1);
  19 + }
  20 +
  21 + stim::network<float> GT;
  22 + GT.load_obj(argv[1]);
  23 +
  24 + std::cout<<GT.str();
  25 +
  26 +
  27 + /*std::string groundTruth = argv[1];
17 28 std::string truthCase = argv[2];
  29 + float sigma = atof(argv[3]);
  30 +
18 31 //stim::network<int> network;
19 32 boost::tuple< ANNkd_tree*, ANNkd_tree*, stim::network<float>, stim::network<float> > networkKdtree;
20 33 networkKdtree = network1->LoadNetworks(groundTruth, truthCase);
21   - //std::cout<<networkKdtree.get< 2>().edges_to_str()<<std::endl;
  34 + std::cout<<networkKdtree.get< 2>().edges_to_str()<<std::endl;
22 35 networkKdtree.get< 2>().to_obj();
23 36 //networkKdtree.get< 2>()
24   - boost::tuple< float, float > metrics = network1->compareSkeletons(networkKdtree);
  37 + boost::tuple< float, float > metrics = network1->compareSkeletons(networkKdtree, sigma);
25 38 std::cout << "False postive rate is " << metrics.get< 0>() << std::endl;
26 39 std::cout << "False negative rate is " << metrics.get< 1>() << std::endl;
  40 + */
27 41 }
... ...