BrainDynamicsUSYD · pausz · Feb 5, 2018 · Feb 2, 2018 · Feb 2, 2018 · Feb 2, 2018
diff --git a/+nf/extract.m b/+nf/extract.m
@@ -1,9 +1,9 @@
-%% Extract a specific subset of data from a neurofield output struct.
+%% Extract a specific subset of data from a nftsim output struct.
 %
 % The subset can be specified in terms of: traces; times; and nodes.
 %
 % ARGUMENTS:
-%        obj -- A neurofield output struct (a Matlab struct containing data
+%        obj -- A nftsim output struct (a Matlab struct containing data
 %               from a simulation).
 %        traces -- A cell array or a comma separated string of the traces
 %                  you want to extract, e.g. 'Propagator.2.phi, Coupling.2.nu'.
@@ -35,7 +35,7 @@
     % If no nodes are provided, output all nodes
     if ~isstruct(obj) || ~isfield(obj, 'data')
         error(['nf:' mfilename ':BadArgument'], ...
-              'The first argument must be a neurofield output struct.');
+              'The first argument must be a nftsim output struct.');
     end
 
     if nargin < 4 || isempty(nodes)

diff --git a/+nf/grid.m b/+nf/grid.m
@@ -8,7 +8,7 @@
 % output all nodes), or the number of nodes is not a perfect square..
 %
 % ARGUMENTS:
-%        obj   -- A neurofield output struct (a Matlab struct containing data
+%        obj   -- A nftsim output struct (a Matlab struct containing data
 %                 from a simulation).
 %        trace -- A string with the name of the array to reshape. 
 %
@@ -35,7 +35,7 @@
 
     if output_nodes ~= obj.input_nodes 
         error(['nf:' mfilename ':IncompatibleOutput'], ...
-              'Output from NeuroField must be for all nodes')
+              'Output from NFTsim must be for all nodes')
     end    
 
     data = nf.extract(obj, trace);

diff --git a/+nf/plot_timeseries.m b/+nf/plot_timeseries.m
@@ -17,7 +17,7 @@
 %    figure_handles -- cell array of figure handles.
 %
 % REQUIRES:
-%    nf.extract() -- Extract a specific subset of data from a neurofield
+%    nf.extract() -- Extract a specific subset of data from a nftsim
 %                    output struct.
 %
 % AUTHOR:
@@ -28,7 +28,7 @@
 %{
     %Either run a simulation:
     nf_obj = nf.run('./configs/eirs-corticothalamic.conf')
-    %Or load some neurofield output data
+    %Or load some nftsim output data
     nf_obj = nf.read('./configs/eirs-corticothalamic.output')
 
     %Plot every fourth node for the trace 'Propagator.1.phi'.

diff --git a/+nf/read.m b/+nf/read.m
@@ -1,11 +1,11 @@
-%% Read a neurofield output file and return a neurofield output struct.
+%% Read a nftsim output file and return a nftsim output struct.
 %
 % ARGUMENTS:
-%        fname -- The name of the neurofield output file to read (absolute
+%        fname -- The name of the nftsim output file to read (absolute
 %                 or relative path).
 %
 % OUTPUT:
-%        obj -- A neurofield output struct. A Matlab struct containing data
+%        obj -- A nftsim output struct. A Matlab struct containing data
 %               and parameters from a simulation.
 %
 % AUTHOR:

diff --git a/+nf/report.m b/+nf/report.m
@@ -1,7 +1,7 @@
-%% Given a neurofield output struct, print some information about it.
+%% Given a nftsim output struct, print some information about it.
 %
 % ARGUMENTS:
-%        obj -- A neurofield output struct (a Matlab struct containing data
+%        obj -- A nftsim output struct (a Matlab struct containing data
 %               from a simulation).
 %
 % OUTPUT: Prints to terminal.
@@ -16,7 +16,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function report(obj)
-    fprintf(1, 'Output for: neurofield -i "%s"\n', obj.conf_file)
+    fprintf(1, 'Output for: nftsim -i "%s"\n', obj.conf_file)
     fprintf(1, 'Traces: ');
     for j = 1:length(obj.fields)
         fprintf(1, '%s ', obj.fields{j});

diff --git a/+nf/run.m b/+nf/run.m
@@ -1,38 +1,38 @@
-%% Function to run neurofield and return a neurofield output struct.
+%% Function to run nftsim and return a nftsim output struct.
 %
-% Provided a configuration file-name (fname.conf), run the neurofield
+% Provided a configuration file-name (fname.conf), run the nftsim
 % executable, generating an output file (fname.output). Optionally, if an
 % output argument is provided then, parse the output file and return a
-% neurofield output struct containing the simulation results.
+% nftsim output struct containing the simulation results.
 %
 %
 % ARGUMENTS:
 %        fname -- Name of the configuration file, it can be with or without
 %                 the .conf extension.
 %        time_stamp -- boolean flag to use a time_stamp YYYY-MM-DDTHHMMSS
 %                      in the output file name.
-%        neurofield_path -- neurofield executable (full or relative path).
+%        nftsim_path -- nftsim executable (full or relative path).
 %
 % OUTPUT: Writes a .output file in the same location as the .conf file.
-%        obj -- A neurofield output struct (a Matlab struct containing
+%        obj -- A nftsim output struct (a Matlab struct containing
 %               data from a simulation).
 %
 % REQUIRES:
-%        neurofield -- The neurofield executable, must be in your path.
-%        nf.read -- Read a neurofield output file and return a neurofield
+%        nftsim -- The nftsim executable, must be in your path.
+%        nf.read -- Read a nftsim output file and return a nftsim
 %                   output struct.
 %
 % AUTHOR:
 %     Romesh Abeysuriya (2012-03-22).
 %
 % USAGE:
 %{
-    %At a matlab command promt, from neurofield's main directory:
+    %At a matlab command promt, from nftsim's main directory:
     nf_obj = nf.run('./configs/eirs-corticothalamic.conf')
 %}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function obj = run(fname, time_stamp, neurofield_path)
+function obj = run(fname, time_stamp, nftsim_path)
     %
     tic;
     fname = strrep(fname, '.conf', ''); %Strip any .conf suffix.
@@ -41,39 +41,39 @@
     if nargin < 2
         time_stamp = false;
     end
-    % If we were not provided a path to neurofield, try to determine one.
-    if nargin < 3 || isempty(neurofield_path)
+    % If we were not provided a path to nftsim, try to determine one.
+    if nargin < 3 || isempty(nftsim_path)
         % Check typical locations, the first path that exists will be selected.
-        locations = {'neurofield', ...
-                     './bin/neurofield', ...
-                     './neurofield/bin/neurofield', ...
-                     'neurofield.exe'};
+        locations = {'nftsim', ...
+                     './bin/nftsim', ...
+                     './nftsim/bin/nftsim', ...
+                     'nftsim.exe'};
         selected_path = find(cellfun(@(name) exist(name, 'file')==2, locations), 1, 'first');
         if ~isempty(selected_path)
-            neurofield_path = locations{selected_path};
+            nftsim_path = locations{selected_path};
         else
             error(['nf:' mfilename ':BadPath'], ...
-                  'neurofield not found. Either change into the neurofield base directory or make a symlink to neurofield in the current directory.');
+                  'nftsim not found. Either change into the nftsim base directory or make a symlink to nftsim in the current directory.');
         end
     % If we were provided a path, check that it is valid.
-    elseif ~exist(neurofield_path, 'file')
+    elseif ~exist(nftsim_path, 'file')
         error(['nf:' mfilename ':BadPath'], ...
-              'The neurofield_path you provided is incorrect:"%s".',neurofield_path);
+              'The nftsim_path you provided is incorrect:"%s".',nftsim_path);
     end
 
     if ~time_stamp
-        neurofield_cmd = sprintf('%s -i %s.conf -o %s.output', neurofield_path, fname, fname);
+        nftsim_cmd = sprintf('%s -i %s.conf -o %s.output', nftsim_path, fname, fname);
     else
-        neurofield_cmd = sprintf('%s -i %s.conf -t', neurofield_path, fname);
+        nftsim_cmd = sprintf('%s -i %s.conf -t', nftsim_path, fname);
     end
     fprintf('INFO: Executing command:\n')    
-    fprintf('%s\n', neurofield_cmd);
-    [status, cmdout] = system(neurofield_cmd);
+    fprintf('%s\n', nftsim_cmd);
+    [status, cmdout] = system(nftsim_cmd);
 
     string(cmdout)
     if status ~= 0
-        error(['nf:' mfilename ':NeurofieldError'], ...
-              'An error occurred while running neurofield!');
+        error(['nf:' mfilename ':NFTsimError'], ...
+              'An error occurred while running nftsim!');
     end
 
     fprintf(1, 'INFO: tic-toc: Took about %.3f seconds\n', toc);

diff --git a/+nf/spectrum.m b/+nf/spectrum.m
@@ -1,7 +1,7 @@
-%% Return the frequency and frequency spectrum of given neurofield output.
+%% Return the frequency and frequency spectrum of given nftsim output.
 %
 % ARGUMENTS:
-%        obj -- A neurofield output struct (a Matlab struct containing data
+%        obj -- A nftsim output struct (a Matlab struct containing data
 %               from a simulation).
 %        traces -- traces to use
 %        n_windows -- number of windows (Default=8).
@@ -12,7 +12,7 @@
 %
 % REQUIRES:
 %        nf.partition() -- Partition a list of n items into m groups.
-%        nf.extract() -- Extract a specific subset of data from a neurofield output struct.
+%        nf.extract() -- Extract a specific subset of data from a nftsim output struct.
 %        nf.rfft() -- Fourier transform.
 %
 % REFERENCES:
@@ -22,7 +22,7 @@
 %
 % USAGE:
 %{
-    %Load some neurofield output data.
+    %Load some nftsim output data.
     obj = nf.read('./configs/example.output')
     %Calculate the mean power spectrum.
     [f, P] = nf.spectrum(obj, 'Propagator.1.phi', [], true, true);
@@ -36,7 +36,7 @@
 function [f, P] = spectrum(obj, traces, n_windows, windowed, detrended)
     if ~isstruct(obj)
         error(['nf:' mfilename ':BadArgument'], ...
-              'The first argument must be a neurofield simulation struct.')
+              'The first argument must be a nftsim simulation struct.')
     end
 
     if nargin < 2 || isempty(traces)

diff --git a/.gitattributes b/.gitattributes
@@ -15,7 +15,7 @@
 Makefile text
 
 # The executable.
-neurofield binary
+nftsim binary
 
 #Configuration files
 *.conf text

diff --git a/.gitignore b/.gitignore
@@ -7,7 +7,7 @@ dep/
 doc/html/
 doc/latex/
 
-# Ignore NeuroField output files
+# Ignore NFTsim output files
 *.output
 *.mat
 

diff --git a/Doxyfile b/Doxyfile
@@ -33,7 +33,7 @@ DOXYFILE_ENCODING      = UTF-8
 # title of most generated pages and in a few other places.
 # The default value is: My Project.
 
-PROJECT_NAME           = "Neurofield"
+PROJECT_NAME           = "NFTsim"
 
 # The PROJECT_NUMBER tag can be used to enter a project or revision number. This
 # could be handy for archiving the generated documentation or if some version

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-#Makefile for neurofield
+#Makefile for nftsim
 #
 #  Type 'make help' for a list of possible targets with brief descriptions.
 #  If you're having problems, the Makefile itself can be debugged using the
@@ -14,7 +14,7 @@ DOCDIR := doc/
 DEPDIR := dep/
 
 #Default to *nix, suffix-less, binary.
-BIN := neurofield
+BIN := nftsim
 
 #User-manual files
 USER_MANUAL := NFTsimManual.pdf
@@ -58,18 +58,18 @@ NO_DEPS += clean-user-manual clean-reference-manual clean-docs clean-deps clean-
 # Define our suffix list
 .SUFFIXES: .o .d .cpp .h .tex
 
-.PHONY: neurofield debug all clang make_bin_dir make_obj_dir make_dep_dir help help-dev info docs user-manual reference-manual \
+.PHONY: nftsim debug all clang make_bin_dir make_obj_dir make_dep_dir help help-dev info docs user-manual reference-manual \
 	clean-user-manual clean-reference-manual clean-docs clean-deps clean-objs clean-bin clean clean-all
 
-# target: neurofield - Compile neurofield placing the executable in the bin directory.
-neurofield: $(BINDIR)$(BIN)
+# target: nftsim - Compile nftsim placing the executable in the bin directory.
+nftsim: $(BINDIR)$(BIN)
 
-# target: debug - Compile neurofield with debugging enabled.
+# target: debug - Compile nftsim with debugging enabled.
 debug: CXXFLAGS := $(DEBUG)
-debug: neurofield
+debug: nftsim
 
-# target: all - Compile neurofield and build all documentation.
-all: neurofield docs
+# target: all - Compile nftsim and build all documentation.
+all: nftsim docs
 
 #   target: gcc - Build using gcc, unnecessary on Linux as gcc is default.
 ifeq ($(MAKECMDGOALS), gcc)
@@ -80,7 +80,7 @@ ifeq ($(MAKECMDGOALS), gcc)
   CXXFLAGS := -std=c++11 -lm -Wall -Wextra -pedantic -msse -msse2 -msse3 -mfpmath=sse -march=native -mtune=native -funroll-loops -flto -O3
   DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
 endif
-gcc: neurofield
+gcc: nftsim
 
 #   target: clang - Build using clang++, unnecessary on MacOS unless you want extra warnings as clang++ is default.
 ifeq ($(MAKECMDGOALS), clang)
@@ -91,7 +91,7 @@ ifeq ($(MAKECMDGOALS), clang)
   CXXFLAGS := -std=c++11 -Weverything -Wno-padded -Wno-c++98-compat -Wno-c++98-compat-pedantic -fdiagnostics-fixit-info -Wdocumentation -march=native -funroll-loops -flto -O3
   DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
 endif
-clang: neurofield
+clang: nftsim
 
 #   target: intel - Build using intel C++ compiler.
 ifeq ($(MAKECMDGOALS), intel)
@@ -104,13 +104,13 @@ ifeq ($(MAKECMDGOALS), intel)
   CXXFLAGS := -std=c++11 -Wall -Wremarks -Wchecks -Weffec++ -xHost -funroll-loops -ipo -O3
   DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
 endif
-intel: neurofield
+intel: nftsim
 
 #   target: $(BINDIR)$(BIN) - Main target for the final build, linking objects into an executable.
 $(BINDIR)$(BIN): $(OBJ) | make_bin_dir
 	$(CXX) $(CXXFLAGS) $(OBJ) -o $@
 	@$(CAT) conditions.txt
-	@echo "USE OF NEUROFIELD CONSTITUTES ACCEPTANCE OF THE APACHE 2.0 LICENSE"
+	@echo "USE OF NFTSIM CONSTITUTES ACCEPTANCE OF THE APACHE 2.0 LICENSE"
 
 #   target: make_bin_dir - Create the directory $BINDIR if it doesn't already exist.
 make_bin_dir:

diff --git a/README.md b/README.md
@@ -36,7 +36,7 @@ To build the executable on Linux or MacOS, open a terminal in the `nftsim` direc
 
     make
 
-this produces the executable `bin/neurofield` and autogenerates the documentation. 
+this produces the executable `bin/nftsim` and autogenerates the documentation. 
 
 To build only the reference manual type:
 
@@ -57,7 +57,7 @@ Example configurations including examples for published results are available in
 
 To run the basic example type
 
-    ./bin/neurofield -i ./configs/eirs-corticothalamic.conf -o eirs-corticothalamic.output
+    ./bin/nftsim -i ./configs/eirs-corticothalamic.conf -o eirs-corticothalamic.output
 
 ## Troubleshooting