Network schema io

.gitignore

@@ -51,3 +51,9 @@ cmake-build-debug/
 cmake-build-release/src/
 
 cmake-build-release/
+
+scripts/ol_api/t1\.csv
+
+scripts/tn_api/__init__.pyc
+
+*.pyc

.gitmodules

@@ -7,3 +7,7 @@
 	path = src/lib/c11t
 	url = https://github.com/jtsiomb/c11threads.git
 
+[submodule "lua"]
+	path = lua
+	url = https://github.com/markplagge/lua.git
+	branch = lua-5.1

.vscode/.ropeproject/config.py

@@ -0,0 +1,100 @@
+# The default ``config.py``
+# flake8: noqa
+
+
+def set_prefs(prefs):
+    """This function is called before opening the project"""
+
+    # Specify which files and folders to ignore in the project.
+    # Changes to ignored resources are not added to the history and
+    # VCSs.  Also they are not returned in `Project.get_files()`.
+    # Note that ``?`` and ``*`` match all characters but slashes.
+    # '*.pyc': matches 'test.pyc' and 'pkg/test.pyc'
+    # 'mod*.pyc': matches 'test/mod1.pyc' but not 'mod/1.pyc'
+    # '.svn': matches 'pkg/.svn' and all of its children
+    # 'build/*.o': matches 'build/lib.o' but not 'build/sub/lib.o'
+    # 'build//*.o': matches 'build/lib.o' and 'build/sub/lib.o'
+    prefs['ignored_resources'] = ['*.pyc', '*~', '.ropeproject',
+                                  '.hg', '.svn', '_svn', '.git', '.tox']
+
+    # Specifies which files should be considered python files.  It is
+    # useful when you have scripts inside your project.  Only files
+    # ending with ``.py`` are considered to be python files by
+    # default.
+    #prefs['python_files'] = ['*.py']
+
+    # Custom source folders:  By default rope searches the project
+    # for finding source folders (folders that should be searched
+    # for finding modules).  You can add paths to that list.  Note
+    # that rope guesses project source folders correctly most of the
+    # time; use this if you have any problems.
+    # The folders should be relative to project root and use '/' for
+    # separating folders regardless of the platform rope is running on.
+    # 'src/my_source_folder' for instance.
+    #prefs.add('source_folders', 'src')
+
+    # You can extend python path for looking up modules
+    #prefs.add('python_path', '~/python/')
+
+    # Should rope save object information or not.
+    prefs['save_objectdb'] = True
+    prefs['compress_objectdb'] = False
+
+    # If `True`, rope analyzes each module when it is being saved.
+    prefs['automatic_soa'] = True
+    # The depth of calls to follow in static object analysis
+    prefs['soa_followed_calls'] = 0
+
+    # If `False` when running modules or unit tests "dynamic object
+    # analysis" is turned off.  This makes them much faster.
+    prefs['perform_doa'] = True
+
+    # Rope can check the validity of its object DB when running.
+    prefs['validate_objectdb'] = True
+
+    # How many undos to hold?
+    prefs['max_history_items'] = 32
+
+    # Shows whether to save history across sessions.
+    prefs['save_history'] = True
+    prefs['compress_history'] = False
+
+    # Set the number spaces used for indenting.  According to
+    # :PEP:`8`, it is best to use 4 spaces.  Since most of rope's
+    # unit-tests use 4 spaces it is more reliable, too.
+    prefs['indent_size'] = 4
+
+    # Builtin and c-extension modules that are allowed to be imported
+    # and inspected by rope.
+    prefs['extension_modules'] = []
+
+    # Add all standard c-extensions to extension_modules list.
+    prefs['import_dynload_stdmods'] = True
+
+    # If `True` modules with syntax errors are considered to be empty.
+    # The default value is `False`; When `False` syntax errors raise
+    # `rope.base.exceptions.ModuleSyntaxError` exception.
+    prefs['ignore_syntax_errors'] = False
+
+    # If `True`, rope ignores unresolvable imports.  Otherwise, they
+    # appear in the importing namespace.
+    prefs['ignore_bad_imports'] = False
+
+    # If `True`, rope will insert new module imports as
+    # `from <package> import <module>` by default.
+    prefs['prefer_module_from_imports'] = False
+
+    # If `True`, rope will transform a comma list of imports into
+    # multiple separate import statements when organizing
+    # imports.
+    prefs['split_imports'] = False
+
+    # If `True`, rope will sort imports alphabetically by module name
+    # instead of alphabetically by import statement, with from imports
+    # after normal imports.
+    prefs['sort_imports_alphabetically'] = False
+
+
+def project_opened(project):
+    """This function is called after opening the project"""
+    # Do whatever you like here!

.vscode/settings.json

@@ -0,0 +1,3 @@
+// Place your settings in this file to overwrite default and user settings.
+{
+}

CMakeLists.txt

@@ -1,22 +1,60 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
+set(CMAKE_C_STANDARD 99)
+ADD_COMPILE_OPTIONS(-std=gnu99)
+#set(CMAKE_C_FLAGS "${CMAKE_C_CFLAGS} -std=gnu99")
 project(SuperNeMo)
 enable_testing()
+include(ExternalProject)
+
 
 set (RD "${CMAKE_CURRENT_SOURCE_DIR}/ROSS/")
 set (ND "${CMAKE_CURRENT_SOURCE_DIR}/src/")
+set (LuaD "${CMAKE_CURRENT_SOURCE_DIR}/lua")
+
 
+#cmake_policy(SET CMP0012 OLD)
+# LUA Options
+#SET(USE_LUA_JIT FALSE BOOL)
+option(USE_LUA_JIT "Use JIT lua project for scripting" OFF)
+#SET(USE_LUA_JIT TRUE)
 ADD_SUBDIRECTORY(${RD})
+
+if(USE_LUA_JIT)
+    message(STATUS "LUA JIT PROJECT" )
+
+else()
+    ADD_SUBDIRECTORY(${LuaD})
+    include_directories(${MPI_INCLUDE_PATH}
+            ${LuaD}/src
+            ${lua_BINARY_DIR})
+endif()
+
+
 ADD_SUBDIRECTORY(${ND})
-find_package(MPI REQUIRED)
-include_directories(${MPI_INCLUDE_PATH})
+#find_package(MPI REQUIRED)
+
+
 
-SET(CMAKE_C_COMPILER mpicc)
-SET(CMAKE_CXX_COMPILER mpicxx)
+#get_target_property(CFLGS ROSS CMAKE_C_FLAGS)
 set_target_properties( NeMo
     PROPERTIES
     ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib"
     LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib"
     RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+    CONFIG_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/scripts"
+        USE_LUA_JIT ${USE_LUA_JIT}
+ #       CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${CFLGS} -std=gnu11"
 )
+
+
+#files for running IO:
+#
+
+
 configure_file("demo.csv" "${CMAKE_BINARY_DIR}/bin/demo.csv" COPYONLY)
+CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/src/IO/model_read.lua ${CMAKE_CURRENT_BINARY_DIR}/bin/model_read.lua COPYONLY)
+CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/src/IO/tn_types.lua ${CMAKE_CURRENT_BINARY_DIR}/bin/tn_types.lua COPYONLY)
+
+
+
 #TODO: Add targets to the build-tree export set

line.csv

@@ -0,0 +1 @@
+TN,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,1,0,0,1,0,1,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,0,0,0,1,1,0,0,0,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,3,2,1,0,0,0,0,

quick_nemo_input_ref.csv

@@ -0,0 +1,31 @@
+Fields:
+type
+coreID
+localID
+//Arrays are first // 
+synapticConnectivity
+SigmaGI
+S
+weight_selection
+// synaptic_weights calculated value
+epsilon
+sigma_l
+lambda
+c
+posThreshold
+negThreshold
+thresholdRPNMask
+VR
+sigmaVR
+resetVoltage (VR)
+resetMode
+kappa
+omega
+signalDelay
+destCore
+destLocal
+//CUSTOM FOR NEMO //
+isOutputNeuron
+isSelfFiring
+isActiveNeuron (true) //////not used! 
+