diff --git a/.travis/travis_build_linux.sh b/.travis/travis_build_linux.sh
index 5530f9a7948b0a9bc1663c81ab30abcb265eb441..3a2ebbfa48f5022d52eb5af6bec4e001ce91025d 100755
--- a/.travis/travis_build_linux.sh
+++ b/.travis/travis_build_linux.sh
@@ -20,20 +20,22 @@
set -o nounset # Treat unset variables as an error
set -e
-PYTHON2="/usr/bin/python2"
-PYTHON3=`which python3`
#MAKEFLAGS="-j 4"
+PYTHON2="/usr/bin/python2"
# Bug: `which python` returns /opt/bin/python* etc on travis. For which numpy
# many not be available. Therefore, it is neccessary to use fixed path for
# python executable.
+PYTHON3="/usr/bin/python3"
(
# Old makefile based flow.
$PYTHON2 -m compileall -q .
if type $PYTHON3 > /dev/null; then $PYTHON3 -m compileall -q . ; fi
- # Traditional make.
- make
+ ## DEPRECATED: No longer testing make file.
+
+ ## Traditional make.
+ #make
## CMAKE based flow
mkdir -p _GSL_BUILD && cd _GSL_BUILD && \
cmake -DDEBUG=ON -DPYTHON_EXECUTABLE="$PYTHON2" ..
diff --git a/VERSION b/VERSION
deleted file mode 100644
index 93738075c8d40e9ffc625dbd7b2f96b6ee4111d0..0000000000000000000000000000000000000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-3.1.1-129-g669b981
\ No newline at end of file
diff --git a/basecode/global.cpp b/basecode/global.cpp
index ec5a523e78e911755e12565e854af321b5172ada..b54fc979131dce4103a106281a28ab23ef0d7375 100644
--- a/basecode/global.cpp
+++ b/basecode/global.cpp
@@ -87,7 +87,7 @@ namespace moose {
*
* @param x
*/
- void mtseed( unsigned int x )
+ void mtseed( int x )
{
moose::__rng_seed__ = x;
moose::rng.setSeed( x );
diff --git a/basecode/global.h b/basecode/global.h
index 9b06b2820245f1ef4d8fd0639be1b3e6f42a5a13..40b2dba5758c8c848e49ecca9a7b92257b4c9d9f 100644
--- a/basecode/global.h
+++ b/basecode/global.h
@@ -109,7 +109,7 @@ namespace moose
*
* @param seed
*/
- void mtseed( unsigned int seed );
+ void mtseed( int seed );
/**
* @brief Generate a random double between 0 and 1
diff --git a/biophysics/ReadSwc.cpp b/biophysics/ReadSwc.cpp
index 9894e0472bf64628f75971fc76ae95f6d2c3ddf6..3fde18ec6c22e432c8d6d7fb405d57aab376b4c1 100644
--- a/biophysics/ReadSwc.cpp
+++ b/biophysics/ReadSwc.cpp
@@ -23,6 +23,7 @@ static const double MinRadius = 0.04;
ReadSwc::ReadSwc( const string& fname )
{
+ bool verbose = false;
ifstream fin( fname.c_str() );
if ( !fin ) {
cerr << "ReadSwc:: could not open file " << fname << endl;
@@ -52,12 +53,13 @@ ReadSwc::ReadSwc( const string& fname )
cleanZeroLength();
parseBranches();
}
- cout << "ReadSwc: " << fname << " : NumSegs = " << segs_.size() <<
+ cout << "ReadSwc: " << fname << " : " << (valid ? "OK" : "FAILED" )<<
+ ", # Branches = " << branches_.size() <<
+ ". # Segs = " << segs_.size() <<
", bad = " << badSegs <<
- ", Validated = " << valid <<
- ", numBranches = " << branches_.size() <<
endl;
- diagnostics();
+ if ( verbose )
+ diagnostics();
}
bool ReadSwc::validate() const
diff --git a/pymoose/CMakeLists.txt b/pymoose/CMakeLists.txt
index 83397de45054b7cc470f3c144ec6632ad3978c05..af4e8e749a827b113267d557ba89f7071277ff14 100644
--- a/pymoose/CMakeLists.txt
+++ b/pymoose/CMakeLists.txt
@@ -1,6 +1,8 @@
add_definitions(-DPYMOOSE)
include_directories(../basecode ../msg)
+find_package( PythonInterp REQUIRED )
+
set(PYMOOSE_SRCS
moosemodule.cpp
vec.cpp
@@ -18,10 +20,18 @@ EXEC_PROGRAM(${PYTHON_EXECUTABLE}
except Exception: pass'"
OUTPUT_VARIABLE PYTHON_SO_EXTENSION
)
+
+message( STATUS "Python path ${PYTHON_EXECUTABLE}" )
message( STATUS "Python so extension ${PYTHON_SO_EXTENSION}" )
find_package(NumPy REQUIRED)
-include_directories(${NUMPY_INCLUDE_DIRS})
+find_package(PythonLibs REQUIRED)
+
+include_directories( ${NUMPY_INCLUDE_DIRS} )
+include_directories( ${PYTHON_INCLUDE_DIRS} )
+
+message( STATUS "Python include dir : ${PYTHON_INCLUDE_DIRS} " )
+
add_definitions(-DUSE_NUMPY)
add_definitions(-DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION)
@@ -34,7 +44,12 @@ execute_process( COMMAND ${PYTHON_EXECUTABLE}-config --libs
OUTPUT_VARIABLE PYTHON_LIBRARIES
OUTPUT_STRIP_TRAILING_WHITESPACE
)
+
+if( NOT PYTHON_INCLUDE_FLAGS )
+ set( PYTHON_INCLUDE_FLAGS "-I ${PYTHON_INCLUDE_DIRS} " )
+endif( )
message( STATUS "Python include flags: ${PYTHON_INCLUDE_FLAGS}" )
+
set_target_properties(_moose PROPERTIES
COMPILE_DEFINITIONS "PYMOOSE"
COMPILE_FLAGS "${PYTHON_INCLUDE_FLAGS}"
@@ -43,11 +58,6 @@ set_target_properties(_moose PROPERTIES
SUFFIX ".so"
)
-#if(NOT(PYTHON_SO_EXTENSION STREQUAL ""))
-# set_target_properties(_moose PROPERTIES
-# SUFFIX ${PYTHON_SO_EXTENSION})
-#endif()
-
# see issue #80
if(HDF5_LIBRARY_DIRS)
set_target_properties( _moose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
diff --git a/python/moose/SBML/readSBML.py b/python/moose/SBML/readSBML.py
index 220442975ced71ad8a5af13e63e256f03eac3a0f..255d96783e4d576b8cbc1430b1d2ba10898b08f3 100644
--- a/python/moose/SBML/readSBML.py
+++ b/python/moose/SBML/readSBML.py
@@ -66,11 +66,12 @@ def mooseReadSBML(filepath, loadpath, solver="ee"):
'\n\t easy_install python-libsbml'
'\n\t apt-get install python-libsbml'
)
- return None
+ return moose.element('/')
if not os.path.isfile(filepath):
print('%s is not found ' % filepath)
- return None
+ return moose.element('/')
+
with open(filepath, "r") as filep:
filep = open(filepath, "r")
diff --git a/python/moose/plot_utils.py b/python/moose/plot_utils.py
index b2740954dc10103f0c6e6f266ce08cb4cedeb315..94c8577e7491f4550f72774303f10e7a9872af1e 100644
--- a/python/moose/plot_utils.py
+++ b/python/moose/plot_utils.py
@@ -135,7 +135,7 @@ def plotTables(tables, outfile=None, **kwargs):
subplot = kwargs.get('subplot', True)
for i, tname in enumerate(tables):
if subplot:
- plt.subplot(len(tables), 1, i)
+ plt.subplot(len(tables), 1, i+1)
yvec = tables[tname].vector
xvec = np.linspace(0, moose.Clock('/clock').currentTime, len(yvec))
plt.plot(xvec, yvec, label=tname)
@@ -165,7 +165,7 @@ def plotVector(vec, xvec = None, **options):
:param vec: Given vector.
:param **kwargs: Optional to pass to maplotlib.
"""
-
+ ax = options[ 'ax' ]
assert type(vec) == np.ndarray, "Expected type %s" % type(vec)
legend = options.get('legend', True)
@@ -176,28 +176,29 @@ def plotVector(vec, xvec = None, **options):
xx = xvec[:]
assert len(xx) == len(vec), "Expecting %s got %s" % (len(vec), len(xvec))
+ ax.plot(xx, vec, label=options.get('label', ''))
- plt.plot(xx, vec, label=options.get('label', ''))
if legend:
# This may not be available on older version of matplotlib.
try:
- plt.legend(loc='best', framealpha=0.4)
+ ax.legend(loc='best', framealpha=0.4)
except:
- plt.legend(loc='best')
+ ax.legend(loc='best')
if xvec is None:
- plt.xlabel('Time (sec)')
+ ax.set_xlabel('Time (sec)')
else:
- plt.xlabel(options.get('xlabel', ''))
+ ax.set_xlabel(options.get('xlabel', ''))
- plt.ylabel = options.get('ylabel', '')
- plt.title(options.get('title', ''))
+ ax.set_ylabel = options.get('ylabel', '')
+ ax.set_title(options.get('title', ''))
if(options.get('legend', True)):
try:
- plt.legend(loc='best', framealpha=0.4, prop={'size' : 9})
+ ax.legend(loc='best', framealpha=0.4, prop={'size' : 9})
except:
- plt.legend(loc='best', prop={'size' : 9})
+ ax.legend(loc='best', prop={'size' : 9})
+ return ax
def saveRecords(records, xvec = None, **kwargs):
@@ -267,7 +268,7 @@ def plotRecords(records, xvec = None, **kwargs):
yvec = dataDict[k].vector
plotVector(yvec, xvec, label=k, **kwargs)
else:
- plt.subplot(len(dataDict), 1, i)
+ kwargs[ 'ax' ] = plt.subplot(len(dataDict), 1, i)
yvec = dataDict[k].vector
plotVector(yvec, xvec, label=k, **kwargs)
@@ -286,9 +287,13 @@ def plotRecords(records, xvec = None, **kwargs):
else:
plt.show()
+def plot_records( data_dict, xvec = None, **kwargs ):
+ """Renamed (deprecated)
+ """
+ return plot_tables( data_dict, xvec, **kwargs )
-def plot_records(data_dict, xvec = None, **kwargs):
- """plot_records Plot given dictionary.
+def plot_tables(data_dict, xvec = None, **kwargs):
+ """plot_tables plots moose.Table stored in a dictionary.
:param data_dict:
:param xvec: If None, use moose.Clock to generate xvec.
@@ -300,7 +305,12 @@ def plot_records(data_dict, xvec = None, **kwargs):
subplot = kwargs.get('subplot', False)
filters = [ x.lower() for x in kwargs.get('filter', [])]
- plt.figure(figsize=(10, 1.5*len(data_dict)))
+ ax = kwargs.get( 'ax', None )
+ if ax is None:
+ plt.figure(figsize=(10, 1.5*len(data_dict)))
+ if not subplot:
+ ax = plt.subplot( 1, 1, 1 )
+
for i, k in enumerate(data_dict):
pu.info("+ Plotting for %s" % k)
plotThis = False
@@ -312,10 +322,10 @@ def plot_records(data_dict, xvec = None, **kwargs):
if plotThis:
if not subplot:
- yvec = data_dict[k]
+ yvec = data_dict[k].vector
plotVector(yvec, xvec, label=k, **kwargs)
else:
- plt.subplot(len(data_dict), 1, i)
+ ax = plt.subplot(len(data_dict), 1, i)
yvec = data_dict[k]
plotVector(yvec, xvec, label=k, **kwargs)
if subplot:
diff --git a/python/rdesigneur/rdesigneur.py b/python/rdesigneur/rdesigneur.py
index ed38fce962dc452e9a32d275c9fd353b6d075f18..632e7ead2a16364e4f6e4154d82a1f75ea6b5a14 100644
--- a/python/rdesigneur/rdesigneur.py
+++ b/python/rdesigneur/rdesigneur.py
@@ -80,6 +80,7 @@ class rdesigneur:
useGssa = True,
combineSegments = True,
stealCellFromLibrary = False,
+ verbose = True,
diffusionLength= 2e-6,
meshLambda = -1.0, #This is a backward compatibility hack
temperature = 32,
@@ -111,6 +112,7 @@ class rdesigneur:
self.useGssa = useGssa
self.combineSegments = combineSegments
self.stealCellFromLibrary = stealCellFromLibrary
+ self.verbose = verbose
self.diffusionLength= diffusionLength
if meshLambda > 0.0:
print("Warning: meshLambda argument is deprecated. Please use 'diffusionLength' instead.\nFor now rdesigneur will accept this argument.")
@@ -201,7 +203,8 @@ class rdesigneur:
self._buildMoogli()
self._buildStims()
self._configureClocks()
- self._printModelStats()
+ if self.verbose:
+ self._printModelStats()
self._savePlots()
except BuildError as msg:
@@ -315,7 +318,8 @@ class rdesigneur:
return True
if moose.exists( '/library/' + protoVec[0] ):
#moose.copy('/library/' + protoVec[0], '/library/', protoVec[1])
- print('renaming /library/' + protoVec[0] + ' to ' + protoVec[1])
+ if self.verbose:
+ print('renaming /library/' + protoVec[0] + ' to ' + protoVec[1])
moose.element( '/library/' + protoVec[0]).name = protoVec[1]
#moose.le( '/library' )
return True
@@ -596,6 +600,7 @@ class rdesigneur:
def _buildMoogli( self ):
knownFields = {
'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)', -80.0, 40.0 ),
+ 'initVm':('CompartmentBase', 'getInitVm', 1000, 'Init. Memb. Potl (mV)', -80.0, 40.0 ),
'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)', -10.0, 10.0 ),
'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)', -10.0, 10.0 ),
'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)', 0.0, 1.0 ),
diff --git a/synapse/CMakeLists.txt b/synapse/CMakeLists.txt
index bb47b9779b8f3d9c7393cd01f44c27f803ee4248..2b7d36221cd5c50d3afa67766da3f403a1cd75c2 100644
--- a/synapse/CMakeLists.txt
+++ b/synapse/CMakeLists.txt
@@ -1,5 +1,18 @@
cmake_minimum_required(VERSION 2.8)
+
include_directories( ../basecode ../utility ../kinetics)
include_directories( ../external/muparser/include/ )
-file(GLOB SYNAPSE_SRCS *.cpp)
+
+set( SYNAPSE_SRCS
+ GraupnerBrunel2012CaPlasticitySynHandler.cpp
+ RollingMatrix.cpp
+ SeqSynHandler.cpp
+ SimpleSynHandler.cpp
+ STDPSynapse.cpp
+ STDPSynHandler.cpp
+ Synapse.cpp
+ SynHandlerBase.cpp
+ testSynapse.cpp
+ )
+
add_library(synapse ${SYNAPSE_SRCS} )
diff --git a/synapse/RollingMatrix.cpp b/synapse/RollingMatrix.cpp
index f4f5193feab6dc2746ec65c94bdaf8e324b55b15..01818a83f98d356536ca787c696a3f67cac6e03d 100644
--- a/synapse/RollingMatrix.cpp
+++ b/synapse/RollingMatrix.cpp
@@ -72,7 +72,7 @@ double RollingMatrix::dotProduct( const vector< double >& input,
unsigned int index = (row + currentStartRow_) % nrows_;
const SparseVector& sv = rows_[index];
unsigned int i2 = input.size()/2;
- unsigned int istart = (startColumn <= i2) ? 0 : startColumn - i2;
+ unsigned int istart = (startColumn >= i2) ? 0 : i2-startColumn;
unsigned int colstart = (startColumn <= i2) ? 0 : startColumn - i2;
unsigned int iend = (sv.size()-startColumn > i2 ) ? input.size() :
i2 - startColumn + sv.size();
diff --git a/synapse/SeqSynHandler.cpp b/synapse/SeqSynHandler.cpp
index e6ca94f8e8bccadd54293ee9267d136bce0cfcb9..f31f91171120706a2c54f1ffc7ecadbe151409af 100644
--- a/synapse/SeqSynHandler.cpp
+++ b/synapse/SeqSynHandler.cpp
@@ -8,6 +8,7 @@
**********************************************************************/
#include <queue>
+#include "global.h"
#include "header.h"
#include "Synapse.h"
#include "SynEvent.h"
@@ -105,6 +106,29 @@ const Cinfo* SeqSynHandler::initCinfo()
&SeqSynHandler::setSequenceScale,
&SeqSynHandler::getSequenceScale
);
+ static ValueFinfo< SeqSynHandler, vector< unsigned int > > synapseOrder(
+ "synapseOrder",
+ "Mapping of synapse input order to spatial order on syn array."
+ "Entries in this vector are indices which must remain smaller "
+ "than numSynapses. The system will fix up if you mess up. "
+ "It does not insist on unique mappings, but these are "
+ "desirable as outcome is undefined for repeated entries.",
+ &SeqSynHandler::setSynapseOrder,
+ &SeqSynHandler::getSynapseOrder
+ );
+ static ValueFinfo< SeqSynHandler, int > synapseOrderOption(
+ "synapseOrderOption",
+ "How to do the synapse order remapping. This rule stays in "
+ "place and guarantees safe mappings even if the number of "
+ "synapses is altered. Options:\n"
+ "-2: User ordering.\n"
+ "-1: Sequential ordering, 0 to numSynapses-1.\n"
+ "0: Random ordering using existing system seed.\n"
+ ">0: Random ordering using seed specified by this number\n"
+ "Default is -1, sequential ordering.",
+ &SeqSynHandler::setSynapseOrderOption,
+ &SeqSynHandler::getSynapseOrderOption
+ );
static ReadOnlyValueFinfo< SeqSynHandler, double > seqActivation(
"seqActivation",
"Reports summed activation of synaptic channel by sequence",
@@ -141,9 +165,11 @@ const Cinfo* SeqSynHandler::initCinfo()
&historyTime, // Field
&sequenceScale, // Field
&baseScale, // Field
- &seqActivation, // Field
+ &synapseOrder, // Field
+ &synapseOrderOption, // Field
+ &seqActivation, // ReadOnlyField
&plasticityScale, // Field
- &weightScaleVec, // Field
+ &weightScaleVec, // ReadOnlyField
&kernel, // ReadOnlyField
&history // ReadOnlyField
};
@@ -172,10 +198,11 @@ SeqSynHandler::SeqSynHandler()
kernelWidth_( 5 ),
historyTime_( 2.0 ),
seqDt_ ( 1.0 ),
- sequenceScale_( 1.0 ),
baseScale_( 0.0 ),
+ sequenceScale_( 1.0 ),
plasticityScale_( 0.0 ),
- seqActivation_( 0.0 )
+ seqActivation_( 0.0 ),
+ synapseOrderOption_( -1 ) // sequential ordering
{
history_.resize( numHistory(), 0 );
}
@@ -208,6 +235,7 @@ void SeqSynHandler::vSetNumSynapses( const unsigned int v )
history_.resize( numHistory(), v );
latestSpikes_.resize( v, 0.0 );
weightScaleVec_.resize( v, 0.0 );
+ refillSynapseOrder( v );
updateKernel();
}
@@ -227,6 +255,65 @@ Synapse* SeqSynHandler::vGetSynapse( unsigned int i )
}
//////////////////////////////////////////////////////////////////////
+
+// Checks for numbers bigger than the size. Replaces with
+// values within the range that have not yet been used.
+void SeqSynHandler::fixSynapseOrder()
+{
+ unsigned int sz = synapseOrder_.size();
+ vector< unsigned int > availableEntries( sz );
+ iota( availableEntries.begin(), availableEntries.end(), 0 );
+ for( unsigned int i = 0; i < sz; ++i ) {
+ if ( synapseOrder_[i] < sz )
+ availableEntries[ synapseOrder_[i] ] = sz;
+ }
+ vector< unsigned int > ae;
+ for( unsigned int i = 0; i < sz; ++i )
+ if ( availableEntries[i] < sz )
+ ae.push_back( availableEntries[i] );
+
+ auto jj = ae.begin();
+ for( unsigned int i = 0; i < sz; ++i ) {
+ if ( synapseOrder_[i] >= sz )
+ synapseOrder_[i] = *jj++;
+ }
+}
+
+// Beautiful snippet from Lukasz Wiklendt on StackOverflow. Returns order
+// of entries in a vector.
+template <typename T> vector<size_t> sort_indexes(const vector<T> &v) {
+ // initialize original index locations
+ vector<size_t> idx(v.size());
+ iota(idx.begin(), idx.end(), 0);
+ // sort indexes based on comparing values in v
+ sort(idx.begin(), idx.end(),
+ [&v](size_t i1, size_t i2) {return v[i1] < v[i2];});
+ return idx;
+}
+
+void SeqSynHandler::refillSynapseOrder( unsigned int newSize )
+{
+ if ( synapseOrderOption_ <= -2 ) { // User order
+ synapseOrder_.resize( newSize, newSize );
+ fixSynapseOrder();
+ } else if ( synapseOrderOption_ == -1 ) { // Ordered
+ synapseOrder_.resize( newSize );
+ for ( unsigned int i = 0 ; i < newSize; ++i )
+ synapseOrder_[i] = i;
+ } else {
+ synapseOrder_.resize( newSize );
+ if ( synapseOrderOption_ > 0 ) { // Specify seed explicitly
+ moose::mtseed( synapseOrderOption_ );
+ }
+ vector< double > x;
+ for ( unsigned int i = 0; i < newSize; ++i )
+ x.push_back( moose::mtrand() );
+ auto idx = sort_indexes< double >( x );
+ for ( unsigned int i = 0; i < newSize; ++i )
+ synapseOrder_[i] = idx[i];
+ }
+}
+
void SeqSynHandler::updateKernel()
{
if ( kernelEquation_ == "" || seqDt_ < 1e-9 || historyTime_ < 1e-9 )
@@ -362,6 +449,29 @@ vector< double > SeqSynHandler::getHistory() const
return ret;
}
+void SeqSynHandler::setSynapseOrder( vector< unsigned int > v )
+{
+ synapseOrder_ = v;
+ fixSynapseOrder();
+ synapseOrderOption_ = -2; // Set the flag to say it is User defined.
+}
+
+vector< unsigned int > SeqSynHandler::getSynapseOrder() const
+{
+ return synapseOrder_;
+}
+
+void SeqSynHandler::setSynapseOrderOption( int v )
+{
+ synapseOrderOption_ = v;
+ refillSynapseOrder( synapseOrder_.size() );
+}
+
+int SeqSynHandler::getSynapseOrderOption() const
+{
+ return synapseOrderOption_;
+}
+
/////////////////////////////////////////////////////////////////////
void SeqSynHandler::addSpike(unsigned int index, double time, double weight)
@@ -373,7 +483,9 @@ void SeqSynHandler::addSpike(unsigned int index, double time, double weight)
// slice. For now, to get it going for LIF neurons, this will do.
// Even in the general case we will probably have a very wide window
// for the latestSpikes slice.
- latestSpikes_[index] += weight;
+ //
+ // Here we reorder the entries in latestSpikes by the synapse order.
+ latestSpikes_[ synapseOrder_[index] ] += weight;
}
unsigned int SeqSynHandler::addSynapse()
diff --git a/synapse/SeqSynHandler.h b/synapse/SeqSynHandler.h
index 73578b0420bbec7c877726bf7aa0831725b5b455..45217ba0c4c6e052de5ae11cbc47d35714554a8b 100644
--- a/synapse/SeqSynHandler.h
+++ b/synapse/SeqSynHandler.h
@@ -59,6 +59,10 @@ class SeqSynHandler: public SynHandlerBase
double getBaseScale() const;
void setSequenceScale( double v );
double getSequenceScale() const;
+ void setSynapseOrder( vector< unsigned int> v );
+ vector< unsigned int> getSynapseOrder() const;
+ void setSynapseOrderOption( int v );
+ int getSynapseOrderOption() const;
double getSeqActivation() const; // summed activation of syn chan
void setPlasticityScale( double v );
double getPlasticityScale() const;
@@ -69,6 +73,8 @@ class SeqSynHandler: public SynHandlerBase
////////////////////////////////////////////////////////////////
// Utility func
int numHistory() const;
+ void refillSynapseOrder( unsigned int newSize );
+ void fixSynapseOrder();
////////////////////////////////////////////////////////////////
static const Cinfo* initCinfo();
private:
@@ -116,8 +122,23 @@ class SeqSynHandler: public SynHandlerBase
vector< double > latestSpikes_;
///////////////////////////////////////////
- vector< vector< double > > kernel_; //Kernel for seq selectivity
- RollingMatrix history_; // Rows = time; cols = synInputs
+ vector< vector< double > > kernel_; ///Kernel for seq selectivity
+ RollingMatrix history_; /// Rows = time; cols = synInputs
+ /**
+ * Remaps synapse order to avoid correlations based on presynaptic
+ * object Id order, or on connection building order. This
+ * undesirable ordering occurs even when random synaptic
+ * projections are used. User can alter as preferred. This is
+ * simply a look up table so that the incoming synapse index is
+ * remapped: index_on_Handler = synapseOrder_[original_syn_index]
+ * This must only have numbers from zero to numSynapses, and should
+ * normally have all the numbers.
+ */
+ vector< unsigned int > synapseOrder_;
+
+ /// Options: -2: User. -1: ordered. 0: random by system seed.
+ /// > 0: Random by seed specified by this number
+ int synapseOrderOption_;
vector< Synapse > synapses_;
priority_queue< PreSynEvent, vector< PreSynEvent >, CompareSynEvent > events_;
diff --git a/synapse/testSynapse.cpp b/synapse/testSynapse.cpp
index 944525ff8506c78105c2ccf811d8e9a78c2c13fd..b39b87bd654e47cd3b03dfd7f8af665b31068715 100644
--- a/synapse/testSynapse.cpp
+++ b/synapse/testSynapse.cpp
@@ -99,32 +99,44 @@ void testRollingMatrix()
for ( int i = 0; i < nr; ++i )
input[i] = i + 1;
- assert( doubleEq( rm.dotProduct( input, 0, 0 ), 0.0 ) );
- assert( doubleEq( rm.dotProduct( input, 1, 0 ), 1.0 ) );
- assert( doubleEq( rm.dotProduct( input, 2, 0 ), 4.0 ) );
- assert( doubleEq( rm.dotProduct( input, 3, 0 ), 9.0 ) );
- assert( doubleEq( rm.dotProduct( input, 4, 0 ), 16.0 ) );
- assert( doubleEq( rm.dotProduct( input, 4, 1 ), 12.0 ) );
- assert( doubleEq( rm.dotProduct( input, 4, 2 ), 8.0 ) );
- assert( doubleEq( rm.dotProduct( input, 4, 3 ), 4.0 ) );
- assert( doubleEq( rm.dotProduct( input, 4, 4 ), 0.0 ) );
-
+ assert( doubleEq( rm.dotProduct( input, 0, 5 ), 0.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 1, 5 ), 1.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 2, 5 ), 4.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 3, 5 ), 9.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 4, 5 ), 16.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 4, 6 ), 12.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 4, 7 ), 8.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 4, 8 ), 4.0 ) );
+ assert( doubleEq( rm.dotProduct( input, 4, 9 ), 0.0 ) );
+
+ // Note that the input and the row are aligned at col=5, the
+ // middle of the input vector.
rm.sumIntoRow( input, 0 ); // input == [1234500000]
vector< double > corr;
rm.correl( corr, input, 4 ); // rm[4] == [00040000]
- assert( doubleEq( corr[0], 16.0 ) );
- assert( doubleEq( corr[1], 12.0 ) );
- assert( doubleEq( corr[2], 8.0 ) );
- assert( doubleEq( corr[3], 4.0 ) );
- assert( doubleEq( corr[4], 0.0 ) );
+ assert( doubleEq( corr[0], 0.0 ) );
+ assert( doubleEq( corr[1], 0.0 ) );
+ assert( doubleEq( corr[2], 0.0 ) );
+ assert( doubleEq( corr[3], 0.0 ) );
+ assert( doubleEq( corr[4], 20.0 ) );
+ assert( doubleEq( corr[5], 16.0 ) );
+ assert( doubleEq( corr[6], 12.0 ) );
+ assert( doubleEq( corr[7], 8.0 ) );
+ assert( doubleEq( corr[8], 4.0 ) );
+ assert( doubleEq( corr[9], 0.0 ) );
corr.assign( corr.size(), 0 );
rm.correl( corr, input, 0 ); // rm[0] == [1234500000]
- assert( doubleEq( corr[0], 55.0 ) );
- assert( doubleEq( corr[1], 40.0 ) );
- assert( doubleEq( corr[2], 26.0 ) );
- assert( doubleEq( corr[3], 14.0 ) );
- assert( doubleEq( corr[4], 5.0 ) );
+ assert( doubleEq( corr[0], 0.0 ) );
+ assert( doubleEq( corr[1], 5.0 ) );
+ assert( doubleEq( corr[2], 14.0 ) );
+ assert( doubleEq( corr[3], 26.0 ) );
+ assert( doubleEq( corr[4], 40.0 ) );
+ assert( doubleEq( corr[5], 55.0 ) );
+ assert( doubleEq( corr[6], 40.0 ) );
+ assert( doubleEq( corr[7], 26.0 ) );
+ assert( doubleEq( corr[8], 14.0 ) );
+ assert( doubleEq( corr[9], 5.0 ) );
cout << "." << flush;
}
@@ -158,14 +170,12 @@ void testSeqSynapse()
cout << "." << flush;
- // FIXME: See issue BhallaLab/moose-core#174
- // ssh.setResponseScale( 1.0 );
+ ssh.setBaseScale( 1.0 );
+ ssh.setSequenceScale( 1.0 );
for ( int i = 0; i < numSyn; ++i ) {
ssh.addSpike( i, 0.0, 1.0 );
}
-
- // FIXME: See issue BhallaLab/moose-core#174
- // ssh.setWeightScale( 1.0 );
+ ssh.setPlasticityScale( 1.0 );
ProcInfo p;
Eref sheller( Id().eref() );
@@ -177,14 +187,13 @@ void testSeqSynapse()
// Here we correlate the vector [1,1,1,1,1,1,1,1,1,1,1] with
// the kernel [4,1,-1,-1,-1]
// Other lines are zeros.
- // Should really make the kernel mapping symmetrical.
- assert( doubleEq( ssh.getSeqActivation(), 28.0 ) );
+ assert( doubleEq( ssh.getSeqActivation(), 14.0 ) );
vector< double > wts = ssh.getWeightScaleVec();
- for ( int i = 0; i < numSyn-4; ++i )
+ for ( int i = 2; i < numSyn-2; ++i )
assert( doubleEq( wts[i], 2.0 ) );
- assert( doubleEq( wts[6], 3 ) ); // Edge effects. Last -1 vanishes.
- assert( doubleEq( wts[7], 4 ) ); // Edge effects.
- assert( doubleEq( wts[8], 5 ) ); // Edge effects.
+ assert( doubleEq( wts[0], -3 ) ); // Edge effects.
+ assert( doubleEq( wts[1], -2 ) ); // Edge effects.
+ assert( doubleEq( wts[8], 3 ) ); // Edge effects.
assert( doubleEq( wts[9], 4 ) ); // Edge effects.
cout << "." << flush;