diff --git a/moose-core/.travis/travis_build_osx.sh b/moose-core/.travis/travis_build_osx.sh
index e710a00eb9f3955b3d9b61f792e8ebb59ff12edb..f021ef26333f8ebbda5a115a72f0812e66c8e9e3 100755
--- a/moose-core/.travis/travis_build_osx.sh
+++ b/moose-core/.travis/travis_build_osx.sh
@@ -21,10 +21,14 @@ set -o nounset # Treat unset variables as an error
set -e
(
- mkdir -p _GSL_BUILD && cd _GSL_BUILD && cmake -DQUIET_MODE=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=`which python` ..
+ mkdir -p _GSL_BUILD && cd _GSL_BUILD \
+ && cmake -DQUIET_MODE=ON -DDEBUG=ON \
+ -DPYTHON_EXECUTABLE=`which python` ..
make && ctest --output-on-failure
cd .. # Now with boost.
- mkdir -p _BOOST_BUILD && cd _BOOST_BUILD && cmake -DWITH_BOOST=ON -DDEBUG=ON -DPYTHON_EXECUTABLE=`which python` ..
+ mkdir -p _BOOST_BUILD && cd _BOOST_BUILD \
+ && cmake -DWITH_BOOST=ON -DDEBUG=ON \
+ -DPYTHON_EXECUTABLE=`which python` ..
make && ctest --output-on-failure
cd ..
)
diff --git a/moose-core/.travis/travis_prepare_osx.sh b/moose-core/.travis/travis_prepare_osx.sh
index 61fdea5b0a4d2f23b16d19ee1d8b1348b69142e5..b7e0fe3f76c1be14ae51101905f2479755e6cd41 100755
--- a/moose-core/.travis/travis_prepare_osx.sh
+++ b/moose-core/.travis/travis_prepare_osx.sh
@@ -19,17 +19,19 @@
set -o nounset # Treat unset variables as an error
set +e
-rvm get head
-brew update
+#rvm get head
+#brew update
#brew outdated cmake || brew install cmake
brew install gsl
brew install hdf5
-brew install homebrew/science/libsbml
+brew install python
+brew install numpy
#brew outdated python || brew install python
#brew outdated numpy || brew install homebrew/python/numpy
-#brew unlink numpy && brew link numpy || echo "Failed to link numpy"
+brew unlink numpy && brew link numpy || echo "Failed to link numpy"
# Numpy caveats
mkdir -p $HOME/Library/Python/2.7/lib/python/site-packages
echo 'import sys; sys.path.insert(1, "/usr/local/lib/python2.7/site-packages")' >> $HOME/Library/Python/2.7/lib/python/site-packages/homebrew.pth
-pip install matplotlib
-
+# ensurepip
+#python -m ensurepip
+pip2 install matplotlib --user
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index 4b4fe8f1a63212e8957cc6b6567d54a03fbb0ac6..edd1d6cd8050b0c5561210bedd9d46975b74cb5c 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -409,9 +409,12 @@ message( STATUS "Platform ${_platform_desc}" )
set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX}")
-if( ${_platform_desc} MATCHES ".*(Ubuntu|Debian).*" )
- list( APPEND EXTRA_ARGS "--install-layout=deb" )
-endif( )
+## NOTE: Disable it here. It must be handled by moose repository CMakeLists.txt
+## which is used in created packages. For normal user, it should install in
+## site-packages.
+#if( ${_platform_desc} MATCHES ".*(Ubuntu|Debian).*" )
+# list( APPEND EXTRA_ARGS "--install-layout=deb" )
+#endif( )
# If make is called with sudo, install in system directories. Otherwise use
# --user to install in user home.
diff --git a/moose-core/basecode/Id.h b/moose-core/basecode/Id.h
index 04bb31523e660bf417281fb130cfa14d770cee90..9aed5e9beac5e6cf1b7ac6b57317d1c00da827db 100644
--- a/moose-core/basecode/Id.h
+++ b/moose-core/basecode/Id.h
@@ -174,4 +174,13 @@ private:
static vector< Element* >& elements();
};
+namespace std {
+ template <> class hash<Id>{
+ public :
+ size_t operator()(const Id &x ) const{
+ return hash<unsigned int>()( x.value() );
+ }
+ };
+}
+
#endif // _ID_H
diff --git a/moose-core/basecode/header.h b/moose-core/basecode/header.h
index 629560048afea7b908aedbe70e5c3c2737dbfb87..595b7f26b6424a3619a3d06812e458c86b81658d 100644
--- a/moose-core/basecode/header.h
+++ b/moose-core/basecode/header.h
@@ -16,6 +16,7 @@
#include <vector>
#include <string>
#include <map>
+#include <unordered_map>
#include <iostream>
#include <sstream>
#include <typeinfo> // used in Conv.h to extract compiler independent typeid
diff --git a/moose-core/biophysics/CompartmentBase.cpp b/moose-core/biophysics/CompartmentBase.cpp
index 94ac948d7fbdaff6a4eae98cfe4b40914ad00f10..1528f54f6cde2ba2d9e54cb0dcf729848e357a5b 100644
--- a/moose-core/biophysics/CompartmentBase.cpp
+++ b/moose-core/biophysics/CompartmentBase.cpp
@@ -636,6 +636,15 @@ void CompartmentBase::displace( double dx, double dy, double dz )
z_ += dz;
}
+static bool hasScaleFormula( const Eref& e ) {
+ vector< Id > kids;
+ Neutral::children( e, kids );
+ for ( vector< Id >::iterator j = kids.begin(); j != kids.end(); j++ )
+ if ( j->element()->getName() == "scaleFormula" )
+ return true;
+ return false;
+}
+
void CompartmentBase::setGeomAndElec( const Eref& e,
double len, double dia )
{
@@ -650,6 +659,8 @@ void CompartmentBase::setGeomAndElec( const Eref& e,
vector< ObjId > chans;
allChildren( e.objId(), ALLDATA, "ISA=ChanBase", chans );
for ( unsigned int i = 0; i < chans.size(); ++i ) {
+ if ( hasScaleFormula( chans[i].eref() ) )
+ continue; // Later we will eval the formula with len and dia
double gbar = Field< double >::get( chans[i], "Gbar" );
gbar *= len * dia / ( length_ * diameter_ );
Field< double >::set( chans[i], "Gbar", gbar );
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index 265635734f0cdc1e94456022614e5a7314321ff3..6a5e42d390dcae427fdc6031541a51becc962d89 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -1111,6 +1111,7 @@ void Neuron::buildElist( const Eref& e,
ObjId oldCwe = shell->getCwe();
shell->setCwe( e.objId() );
wildcardFind( path, elist );
+ sort( elist.begin(), elist.end() );
shell->setCwe( oldCwe );
evalExprForElist( elist, expr, val );
}
@@ -1285,6 +1286,8 @@ static void fillSegments( vector< SwcSegment >& segs,
comptType = 3; // generic dendrite
}
}
+ // cout << "Seg[" << i << "].xy = " << int(x*1e6) << " " << int(y*1e6) << endl;
+
segs.push_back(
SwcSegment( i, comptType, x, y, z, dia/2.0, paIndex ) );
}
@@ -1347,6 +1350,7 @@ void Neuron::buildSegmentTree( const Eref& e )
{
vector< Id > kids;
Neutral::children( e, kids );
+ sort( kids.begin(), kids.end() );
soma_ = fillSegIndex( kids, segIndex_ );
if ( kids.size() == 0 || soma_ == Id() )
diff --git a/moose-core/ksolve/ZombieEnz.cpp b/moose-core/ksolve/ZombieEnz.cpp
index 8e56b9c7a67c0a7489664d5d73477878073a610b..361ac111f64eefa17f2bfda8c5eb68c06304f747 100644
--- a/moose-core/ksolve/ZombieEnz.cpp
+++ b/moose-core/ksolve/ZombieEnz.cpp
@@ -224,22 +224,28 @@ void ZombieEnz::setSolver( Id stoich, Id enz )
bool isOK = true;
unsigned int numReactants;
numReactants = enz.element()->getNeighbors( enzMols, enzFinfo );
- isOK &= ( numReactants == 1 );
+ bool hasEnz = ( numReactants == 1 );
vector< Id > subs;
numReactants = enz.element()->getNeighbors( subs, subFinfo );
- isOK &= ( numReactants > 0 );
+ bool hasSubs = ( numReactants > 0 );
numReactants = enz.element()->getNeighbors( cplxMols, cplxFinfo );
- isOK &= ( numReactants == 1 );
+ bool hasCplx = ( numReactants == 1 );
vector< Id > prds;
numReactants = enz.element()->getNeighbors( prds, prdFinfo );
- isOK &= ( numReactants > 0 );
+ bool hasPrds = ( numReactants > 0 );
assert( stoich.element()->cinfo()->isA( "Stoich" ) );
stoich_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
- if ( isOK ) {
+ if ( hasEnz && hasSubs && hasCplx && hasPrds ) {
stoich_->installEnzyme( enz, enzMols[0], cplxMols[0], subs, prds );
} else {
stoich_->installDummyEnzyme( enz, Id() );
- cout << "Warning: ZombieEnz:setSolver: Dangling Enz, missing a substrate or product\n";
+ string msg = "";
+ if ( !hasEnz ) msg = msg + " enzyme";
+ if ( !hasCplx ) msg = msg + " enzyme-substrate complex";
+ if ( !hasSubs ) msg = msg + " substrates";
+ if ( !hasPrds ) msg = msg + " products";
+ cout << "Warning: ZombieEnz:setSolver: Dangling Enz '" <<
+ enz.path() << "':\nMissing " << msg << endl;
}
}
diff --git a/moose-core/mesh/NeuroMesh.cpp b/moose-core/mesh/NeuroMesh.cpp
index 968c6c833e5aa29cc871b11609fe7a54c7005f0d..2cf28411d06d8df1ed5d2b0edf922279e0eb2245 100644
--- a/moose-core/mesh/NeuroMesh.cpp
+++ b/moose-core/mesh/NeuroMesh.cpp
@@ -648,6 +648,7 @@ void NeuroMesh::updateShaftParents()
// Uses all compartments, and if they have spines on them adds those too.
void NeuroMesh::setSubTree( const Eref& e, vector< ObjId > compts )
{
+ sort( compts.begin(), compts.end() );
if ( separateSpines_ )
{
NeuroNode::buildSpinyTree( compts, nodes_, shaft_, head_, parent_);
diff --git a/moose-core/mesh/NeuroNode.cpp b/moose-core/mesh/NeuroNode.cpp
index 6afac30e72f6d9ee32f9dc000c3f3a6a94db4e04..9e86634acaf067e232023a23daba1e53f2035476 100644
--- a/moose-core/mesh/NeuroNode.cpp
+++ b/moose-core/mesh/NeuroNode.cpp
@@ -427,7 +427,7 @@ static bool checkForSpine( unsigned int dendIndex, Id compt,
*
*/
static void spinyTraverse( unsigned int dendIndex,
- vector< Id >& dend, const map< Id, unsigned int >& dendMap,
+ vector< Id >& dend, const unordered_map< Id, unsigned int >& dendMap,
vector< int >& seen, unsigned int numSeen,
vector< Id >& shaftId, vector< Id >& headId,
vector< int >& dendParent, vector< unsigned int >& spineParent
@@ -436,7 +436,7 @@ static void spinyTraverse( unsigned int dendIndex,
vector< Id > conn = findAllConnectedCompartments( dend[dendIndex] );
seen[ dendIndex ] = numSeen;
for ( vector< Id >::iterator i = conn.begin(); i != conn.end(); ++i ) {
- map< Id, unsigned int >::const_iterator idLookup =
+ unordered_map< Id, unsigned int >::const_iterator idLookup =
dendMap.find( *i );
if ( idLookup != dendMap.end() ) {
if ( !seen[ idLookup->second ] ) {
@@ -451,6 +451,32 @@ static void spinyTraverse( unsigned int dendIndex,
}
}
+// Takes all 3 arrays, gets an array of indices that sorts them by shaftId,
+// and then uses it to sort them all.
+// Based on a post by quantdev on StackOverflow.
+static void sortByShaftIds( vector< Id >& shaftId, vector< Id >& headId,
+ vector< unsigned int >& spineParent )
+{
+ size_t sortedIndex(0);
+ vector<int> y(shaftId.size());
+ generate(begin(y), end(y), [&]{ return sortedIndex++; });
+ sort( begin(y), end(y),
+ [&](int i1, int i2) { return shaftId[i1] < shaftId[i2]; } );
+
+ assert( sortedIndex == shaftId.size() );
+ assert( sortedIndex == headId.size() );
+ assert( sortedIndex == spineParent.size() );
+
+ auto a = shaftId;
+ auto b = headId;
+ auto c = spineParent;
+ for ( size_t i = 0; i < sortedIndex; ++i) {
+ shaftId[i] = a[y[i]];
+ headId[i] = b[y[i]];
+ spineParent[i] = c[y[i]];
+ }
+}
+
/**
* This function takes a list of elements and builds a tree.
* Info on any attached spines are placed in the
@@ -469,12 +495,13 @@ void NeuroNode::buildSpinyTree(
{
nodes.clear();
sort( elist.begin(), elist.end() );
- map< Id, unsigned int > dendMap;
+ unordered_map< Id, unsigned int > dendMap;
vector< Id > dend;
for ( vector< ObjId >::iterator
i = elist.begin(); i != elist.end(); ++i ) {
if ( isPartOfDend( *i ) ) {
dendMap[ *i ] = dend.size();
+ //cout << "st: dendMap[" << *i << "] = " << dend.size() << endl;
dend.push_back( *i );
}
}
@@ -487,6 +514,9 @@ void NeuroNode::buildSpinyTree(
shaftId, headId,
dendParent, spineParent );
}
+ // Here I sort by shaftIds. I have 4 parallel arrays, so I get the
+ // Index order of the whole lot that will sort the shaftIds.
+ sortByShaftIds( shaftId, headId, spineParent );
if ( numSeen == 0 )
return;
for ( unsigned int i = 0; i < dend.size(); ++i )
@@ -501,10 +531,10 @@ void NeuroNode::buildSpinyTree(
}
void NeuroNode::setParentAndChildren( unsigned int index, int dendParent,
- vector< NeuroNode >& nodes, const map< Id, unsigned int >& dendMap )
+ vector< NeuroNode >& nodes, const unordered_map< Id, unsigned int >& dendMap )
{
parent_ = dendParent;
- const map< Id, unsigned int >::const_iterator dendLookup =
+ const unordered_map< Id, unsigned int >::const_iterator dendLookup =
dendMap.find( nodes[dendParent].elecCompt_ );
if ( dendLookup != dendMap.end() ) {
assert( dendLookup->second < nodes.size() );
diff --git a/moose-core/mesh/NeuroNode.h b/moose-core/mesh/NeuroNode.h
index bb6b5aace1df1c705203947577433e5115be34e6..9c784fcbaabd9429193faffa25617ec3e50f3f7a 100644
--- a/moose-core/mesh/NeuroNode.h
+++ b/moose-core/mesh/NeuroNode.h
@@ -165,7 +165,7 @@ class NeuroNode: public CylBase
vector< unsigned int >& spineParent );
void setParentAndChildren( unsigned int index, int dendParent,
vector< NeuroNode >& nodes,
- const map< Id, unsigned int >& dendMap );
+ const unordered_map< Id, unsigned int >& dendMap );
/**
* Trims off all spines from tree. Does so by identifying a set of
diff --git a/moose-core/mesh/SpineMesh.cpp b/moose-core/mesh/SpineMesh.cpp
index a09c3ccde82a1c4121a65edafc3a58bc1c443695..4fca087264fe7e29ee46db92010529ffd8df98a6 100644
--- a/moose-core/mesh/SpineMesh.cpp
+++ b/moose-core/mesh/SpineMesh.cpp
@@ -260,6 +260,7 @@ void SpineMesh::handleSpineList(
vector< unsigned int > index( head.size(), 0 );
for ( unsigned int i = 0; i < head.size(); ++i ) {
spines_[i] = SpineEntry( shaft[i], head[i], parentVoxel[i] );
+ // cout << i << " " << head[i] << ", pa = " << parentVoxel[i] << endl;
// ret = spines_[i].psdCoords();
// assert( ret.size() == 8 );
// psdCoords.insert( psdCoords.end(), ret.begin(), ret.end() );
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 375fe76dec4b290b0e68c85c65370df6cef148cb..8665281d89c7954d9828930c5e492c18c59e5930 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -527,9 +527,14 @@ class rdesigneur:
cc = moose.element( self.modelPath + '/chem/' + chemCompt)
voxelVec = []
temp = [ self._makeUniqueNameStr( i ) for i in comptList ]
+ #print( temp )
+ #print( "#####################" )
comptSet = set( temp )
#em = [ moose.element(i) for i in cc.elecComptMap ]
- em = [ self._makeUniqueNameStr(i) for i in cc.elecComptMap ]
+ em = sorted( [ self._makeUniqueNameStr(i[0]) for i in cc.elecComptMap ] )
+ #print( em )
+ #print( "=================================================" )
+
voxelVec = [i for i in range(len( em ) ) if em[i] in comptSet ]
# Here we collapse the voxelVec into objects to plot.
allObj = moose.vec( self.modelPath + '/chem/' + plotSpec[2] )
@@ -574,6 +579,7 @@ class rdesigneur:
assert( plotField == plotField2 )
plotObj3 = plotObj + plotObj2
numPlots = sum( q != dummy for q in plotObj3 )
+ #print( "PlotList: {0}: numobj={1}, field ={2}, nd={3}, ns={4}".format( pair, numPlots, plotField, len( dendCompts ), len( spineCompts ) ) )
if numPlots > 0:
tabname = graphs.path + '/plot' + str(k)
scale = knownFields[i[3]][2]
@@ -911,7 +917,6 @@ class rdesigneur:
################################################################
# Utility function for setting up clocks.
def _configureClocks( self ):
- t0 = time.time()
if self.turnOffElec:
elecDt = 1e6
elecPlotDt = 1e6
@@ -920,21 +925,16 @@ class rdesigneur:
elecPlotDt = self.elecPlotDt
diffDt = self.diffDt
chemDt = self.chemDt
- print( "t1 = {}".format( time.time() - t0 ) )
for i in range( 0, 9 ):
moose.setClock( i, elecDt )
moose.setClock( 8, elecPlotDt )
moose.setClock( 10, diffDt )
- print( "t2 = {}".format( time.time() - t0 ) )
for i in range( 11, 18 ):
moose.setClock( i, chemDt )
moose.setClock( 18, self.chemPlotDt )
- print( "t3 = {}".format( time.time() - t0 ) )
hsolve = moose.HSolve( self.elecid.path + '/hsolve' )
hsolve.dt = elecDt
- print( "t4 = {}".format( time.time() - t0 ) )
hsolve.target = self.soma.path
- print( "t5 = {}".format( time.time() - t0 ) )
sys.stdout.flush()
################################################################
################################################################
diff --git a/moose-core/python/setup.cmake.py b/moose-core/python/setup.cmake.py
index 6ba579883d70c713eb21b00068573435048b75a5..54bcc4257a3364dfa1d2dc5089ecf2449ec2e3c2 100644
--- a/moose-core/python/setup.cmake.py
+++ b/moose-core/python/setup.cmake.py
@@ -18,33 +18,11 @@ __status__ = "Development"
import os
import sys
-import site
-
-# if uid is zero then install in root paths. Else install it in user path.
-
-#print( '[INFO] Overwriting --prefix ' )
-#try:
-# prefixLoc = sys.argv.index( '--prefix' )
-# del sys.argv[ prefixLoc ]
-# del sys.argv[ prefixLoc ]
-#except Exception as e:
-# pass
-#
-#uid = os.getuid( )
-#if uid == 0:
-# # Here comes the root.
-# print( ' called by sudo' )
-# sys.argv += [ '--prefix', '/usr' ]
-#else:
-# sys.argv += [ '--prefix', site.getuserbase( ) ]
-#
-#print( sys.argv )
from distutils.core import setup
-
script_dir = os.path.dirname( os.path.abspath( __file__ ) )
-
version = '3.2.git'
+
try:
with open( os.path.join( script_dir, '..', 'VERSION'), 'r' ) as f:
version = f.read( )