From ba782a962d4641a0f4eec7ea0d040104a6f354e4 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawar@users.noreply.github.com>
Date: Tue, 18 Sep 2018 10:48:30 +0530
Subject: [PATCH] Pulled in changes on Sep 17, 2018 (#242)
* Squashed 'moose-core/' changes from d229eba6bb..ec06b242ae
ec06b242ae HotFix: Fix regression in StreadyState solver caused by #293. (#304)
385a5cf0a1 Merge pull request #303 from upibhalla/master
080767c5aa Fixes to rdesigneur due to bad merge. Cleanup on rmoogli
62f8bc89e0 Tweak to Neuron.cpp so it can handle insertion of spines with uniform spacing.
342092829c Update moose_test.py (#301)
f1230f1518 Merge branch 'master' of https://github.com/upibhalla/moose-core
23a2892cc8 Merge branch 'master' of https://github.com/BhallaLab/moose-core
8a835c1332 minor bugfix to rdesigneur
6ef1d567ec Merge branch 'master' into master
a9a2e758ff Merge branch 'master' of https://github.com/BhallaLab/moose-core
5e1294d991 Further updates to rdesigneur for argument handling
a702bded54 Put in kwargs based specification of plotList, stimList and moogList. Folded savePlots into plotList but not yet tested.
git-subtree-dir: moose-core
git-subtree-split: ec06b242ae650f413d50b9c22b76381a94efcba4
* Squashed 'moose-examples/' changes from 2d9849222d..e30d87a637
e30d87a637 Merge pull request #47 from BhallaLab/nml2
e350e8a801 Fixed path in script.
1602f54763 Added missing NML files and removed unneccessary files.
6d6c27e051 nml2 snippets.
3963e7969a Merge pull request #46 from upibhalla/master
4165c53e4a Merge branch 'master' of https://github.com/BhallaLab/moose-examples
2c0afa8fcc Clean up of ephys1 and ephys2 tutorials
9793e59f6c Merge branch 'master' of https://github.com/BhallaLab/moose-examples
2e91700547 Merge pull request #45 from upibhalla/master
7420933455 Added missing image file
70a3b3fc1c Test with python2.7, python3.6 and python3.7 .
bf6c180ee1 Use pypi nightly version to test.
075d01c1af Merge pull request #44 from upibhalla/master
13da78cfc0 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
e3cd31b515 Added Ephys demo for Rall's Law
2e12a9b42a Added squid demo with pyqt5.
410103e36a Use moose.element to get the element.
8f71469d17 Merge pull request #42 from upibhalla/master
77f6694e0e cleanup of some rdesigneur tutorials
9a6f8e214e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
cc44a7e4fb Added demo for uniform spine placement, and putting them in a spiral
3a25620865 First commit for Electrophys tutorial directory
1502a55070 removed old script.
3b7a109b5e Merge branch 'master' of https://github.com/BhallaLab/moose-examples
4336dc3ae8 Fixed passiveDistrib argument list, got rid of unused '.' argument in a few examples
c5e895f30e Updated ex7.5 and README
9f95a87909 Merge branch 'master' of https://github.com/BhallaLab/moose-examples
9ce8913fa5 Added 3 demos for dendritic transport
git-subtree-dir: moose-examples
git-subtree-split: e30d87a6374107d7f0494587dd3d868a22a58e20
* Squashed 'moose-gui/' changes from d226931e0b..c29cede420
c29cede420 hen vertical or horizontal layout is applied for group, compartment size is recalculated
d76d66af1d Function moved to place other than parentpool location its pullback
d03482329c color field is not editable for compartment, enzcplxpool and reaction
0a4b1cab43 compartment boundary is selected if its inside another compartment interior
02b9d3964f comparment size is calculated based on group sceneBoundingRect
8dae832c35 kkitViewcontrol both the groups size are updated if moved from-to is different
44b53bc56d default: addSolver->mooseAddChemSolver, kkitViewcontrol: while rubberbandselection if entire group is selected then delete if partly selected then delete all the items under the selection
80b599f85d mgui: is popup exist then close, objectedit: objectwindowTitle is updated with name when changed, kkit: in positionChange all the neutral is updated with size, kkitViewcontrol:when moose object is moved from Compt/group to group/compartment then mooseobject path is set and for qgraphicalItem and qlineitem objects the parentItem is set which will be grpItem or comptItem
git-subtree-dir: moose-gui
git-subtree-split: c29cede4201bd25dfe868aaaa9d227ea455410ae
---
moose-core/CMakeLists.txt | 1 +
moose-core/biophysics/Neuron.cpp | 30 +-
moose-core/ksolve/Ksolve.cpp | 16 +-
moose-core/ksolve/OdeSystem.h | 9 +-
moose-core/ksolve/SteadyStateBoost.cpp | 121 +--
moose-core/ksolve/SteadyStateGsl.cpp | 138 +--
moose-core/ksolve/VoxelPools.cpp | 142 +--
moose-core/ksolve/VoxelPools.h | 4 +-
moose-core/python/rdesigneur/rdesigneur.py | 448 +++++----
moose-core/python/rdesigneur/rmoogli.py | 2 +-
.../tests/python/chem_models/19085.cspace | 1 +
.../python/testdisabled_dose_response.py | 106 +++
moose-examples/.travis.yml | 15 +-
moose-examples/.travis_prepare.sh | 16 -
.../neuroml2/NML2_SingleCompHHCell.nml | 90 ++
moose-examples/neuroml2/converter.py | 209 +++++
moose-examples/neuroml2/passiveCell.nml | 52 ++
moose-examples/neuroml2/run_cell.py | 112 +++
moose-examples/neuroml2/run_hhcell.py | 151 +++
moose-examples/squid/squid.py | 12 +-
moose-examples/squid/squid_demo.py | 19 +-
moose-examples/squid/squid_demo_qt5.py | 861 ++++++++++++++++++
moose-examples/squid/test_squid.py | 2 +-
.../Electrophys/CableInjectEquivCkt.png | Bin 0 -> 31378 bytes
.../tutorials/Electrophys/README.txt | 80 ++
.../tutorials/Electrophys/RallsLaw.png | Bin 0 -> 41208 bytes
.../tutorials/Electrophys/ephys1_cable.py | 212 +++++
.../tutorials/Electrophys/ephys2_Rall_law.py | 268 ++++++
.../tutorials/Rdesigneur/README.txt | 10 +
.../Rdesigneur/ex3.2_squid_axon_propgn.py | 4 +-
.../Rdesigneur/ex3.3_AP_collision.py | 2 +-
.../Rdesigneur/ex3.4_myelinated_axon.py | 6 -
.../tutorials/Rdesigneur/ex7.2_CICR.py | 1 +
.../Rdesigneur/ex9.3_spiral_spines.py | 19 +
moose-gui/objectedit.py | 12 +-
moose-gui/plugins/kkit.py | 20 +-
moose-gui/plugins/kkitUtil.py | 31 +-
moose-gui/plugins/kkitViewcontrol.py | 26 +-
38 files changed, 2661 insertions(+), 587 deletions(-)
create mode 100644 moose-core/tests/python/chem_models/19085.cspace
create mode 100644 moose-core/tests/python/testdisabled_dose_response.py
delete mode 100755 moose-examples/.travis_prepare.sh
create mode 100644 moose-examples/neuroml2/NML2_SingleCompHHCell.nml
create mode 100644 moose-examples/neuroml2/converter.py
create mode 100644 moose-examples/neuroml2/passiveCell.nml
create mode 100644 moose-examples/neuroml2/run_cell.py
create mode 100644 moose-examples/neuroml2/run_hhcell.py
create mode 100644 moose-examples/squid/squid_demo_qt5.py
create mode 100644 moose-examples/tutorials/Electrophys/CableInjectEquivCkt.png
create mode 100644 moose-examples/tutorials/Electrophys/README.txt
create mode 100644 moose-examples/tutorials/Electrophys/RallsLaw.png
create mode 100644 moose-examples/tutorials/Electrophys/ephys1_cable.py
create mode 100644 moose-examples/tutorials/Electrophys/ephys2_Rall_law.py
create mode 100644 moose-examples/tutorials/Rdesigneur/ex9.3_spiral_spines.py
diff --git a/moose-core/CMakeLists.txt b/moose-core/CMakeLists.txt
index 9bf8255c..3be4235b 100644
--- a/moose-core/CMakeLists.txt
+++ b/moose-core/CMakeLists.txt
@@ -130,6 +130,7 @@ include_directories( ${CMAKE_CURRENT_SOURCE_DIR} )
if(WITH_BOOST)
set(WITH_BOOST_ODE ON)
+ set(WITH_GSL OFF)
endif(WITH_BOOST)
# If using BOOST ODE2 library to solve ODE system, then don't use GSL.
diff --git a/moose-core/biophysics/Neuron.cpp b/moose-core/biophysics/Neuron.cpp
index aa867591..3fbab6d0 100644
--- a/moose-core/biophysics/Neuron.cpp
+++ b/moose-core/biophysics/Neuron.cpp
@@ -315,11 +315,17 @@ const Cinfo* Neuron::initCinfo()
"The expression for the *spacing* field must evaluate to > 0 for "
"the spine to be installed. For example, if the expresssion is\n"
" H(1 - L) \n"
- "then the systemwill only put spines closer than "
+ "then the system will only put spines closer than "
"one length constant from the soma, and zero elsewhere. \n"
"Available spine parameters are: \n"
"spacing, minSpacing, size, sizeDistrib "
- "angle, angleDistrib \n",
+ "angle, angleDistrib \n"
+ "minSpacing sets the granularity of sampling (typically about 0.1*"
+ "spacing) for the usual case where spines are spaced randomly. "
+ "If minSpacing < 0 then the spines are spaced equally at "
+ "'spacing', unless the dendritic segment length is smaller than "
+ "'spacing'. In that case it falls back to the regular random "
+ "placement method.",
&Neuron::setSpineDistribution,
&Neuron::getSpineDistribution
);
@@ -1788,6 +1794,19 @@ static void addPos( unsigned int segIndex, unsigned int eIndex,
vector< unsigned int >& elistIndex,
vector< double >& pos )
{
+ if ( minSpacing < 0.0 ) {
+ // Use uniform spacing
+ for ( double position = spacing * 0.5;
+ position < dendLength; position += spacing ) {
+ seglistIndex.push_back( segIndex );
+ elistIndex.push_back( eIndex );
+ pos.push_back( position );
+ }
+ if ( dendLength > spacing * 0.5 )
+ return;
+ // If the dend length is too small for regular placement,
+ // fall back to using probability to decide if segment gets spine
+ }
if ( minSpacing < spacing * 0.1 && minSpacing < 1e-7 )
minSpacing = spacing * 0.1;
if ( minSpacing > spacing * 0.5 )
@@ -1860,13 +1879,6 @@ void Neuron::makeSpacingDistrib( const vector< ObjId >& elist,
{
double spacing = val[ j + nuParser::EXPR ];
double spacingDistrib = parser.eval( val.begin() + j );
- if ( spacingDistrib > spacing || spacingDistrib < 0 )
- {
- cout << "Warning: Neuron::makeSpacingDistrib: " <<
- "0 < " << spacingDistrib << " < " << spacing <<
- " fails on " << elist[i].path() << ". Using 0.\n";
- spacingDistrib = 0.0;
- }
map< Id, unsigned int>::const_iterator
lookupDend = segIndex_.find( elist[i] );
if ( lookupDend != segIndex_.end() )
diff --git a/moose-core/ksolve/Ksolve.cpp b/moose-core/ksolve/Ksolve.cpp
index 2277e5ff..81bc118f 100644
--- a/moose-core/ksolve/Ksolve.cpp
+++ b/moose-core/ksolve/Ksolve.cpp
@@ -235,7 +235,7 @@ static const Cinfo* ksolveCinfo = Ksolve::initCinfo();
Ksolve::Ksolve()
:
-#if USE_GSL
+#ifdef USE_GSL
method_( "rk5" ),
#elif USE_BOOST_ODE
method_( "rk5a" ),
@@ -248,19 +248,12 @@ Ksolve::Ksolve()
dsolve_(),
dsolvePtr_( 0 )
{
+ ;
}
Ksolve::~Ksolve()
{
-#if 0
- char* p = getenv( "MOOSE_SHOW_SOLVER_PERF" );
- if( p != NULL )
- {
- cout << "Info: Ksolve (+Dsolve) took " << totalTime_ << " seconds and took " << numSteps_
- << " steps." << endl;
-
- }
-#endif
+ ;
}
//////////////////////////////////////////////////////////////
@@ -378,6 +371,7 @@ void Ksolve::setStoich( Id stoich )
assert( stoich.element()->cinfo()->isA( "Stoich" ) );
stoich_ = stoich;
stoichPtr_ = reinterpret_cast< Stoich* >( stoich.eref().data() );
+
if ( !isBuilt_ )
{
OdeSystem ode;
@@ -386,6 +380,7 @@ void Ksolve::setStoich( Id stoich )
// ode.initStepSize = getEstimatedDt();
ode.initStepSize = 0.01; // This will be overridden at reinit.
ode.method = method_;
+
#ifdef USE_GSL
ode.gslSys.dimension = stoichPtr_->getNumAllPools();
if ( ode.gslSys.dimension == 0 )
@@ -416,6 +411,7 @@ void Ksolve::setStoich( Id stoich )
#endif
isBuilt_ = true;
}
+
}
Id Ksolve::getDsolve() const
diff --git a/moose-core/ksolve/OdeSystem.h b/moose-core/ksolve/OdeSystem.h
index 6a3ede6d..511513b5 100644
--- a/moose-core/ksolve/OdeSystem.h
+++ b/moose-core/ksolve/OdeSystem.h
@@ -26,15 +26,16 @@ class OdeSystem {
{;}
std::string method;
- // GSL stuff
+
+ double initStepSize;
+ double epsAbs; // Absolute error
+ double epsRel; // Relative error
#ifdef USE_GSL
+ // GSL stuff
gsl_odeiv2_system gslSys;
const gsl_odeiv2_step_type* gslStep;
#endif
- double initStepSize;
- double epsAbs; // Absolute error
- double epsRel; // Relative error
#if USE_BOOST_ODE
size_t dimension;
diff --git a/moose-core/ksolve/SteadyStateBoost.cpp b/moose-core/ksolve/SteadyStateBoost.cpp
index a96439ba..5d31165d 100644
--- a/moose-core/ksolve/SteadyStateBoost.cpp
+++ b/moose-core/ksolve/SteadyStateBoost.cpp
@@ -85,27 +85,6 @@ struct reac_info
const Cinfo* SteadyState::initCinfo()
{
- /**
- * This picks up the entire Stoich data structure
- static Finfo* gslShared[] =
- {
- new SrcFinfo( "reinitSrc", Ftype0() ),
- new DestFinfo( "assignStoich",
- Ftype1< void* >(),
- RFCAST( &SteadyState::assignStoichFunc )
- ),
- new DestFinfo( "setMolN",
- Ftype2< double, unsigned int >(),
- RFCAST( &SteadyState::setMolN )
- ),
- new SrcFinfo( "requestYsrc", Ftype0() ),
- new DestFinfo( "assignY",
- Ftype1< double* >(),
- RFCAST( &SteadyState::assignY )
- ),
- };
- */
-
/**
* These are the fields of the SteadyState class
*/
@@ -207,59 +186,59 @@ const Cinfo* SteadyState::initCinfo()
// MsgDest definitions
///////////////////////////////////////////////////////
static DestFinfo setupMatrix( "setupMatrix",
- "This function initializes and rebuilds the matrices used "
- "in the calculation.",
- new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
- );
+ "This function initializes and rebuilds the matrices used "
+ "in the calculation.",
+ new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
+ );
static DestFinfo settle( "settle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation "
- "only if the object has not yet been initialized.",
- new OpFunc0< SteadyState >( &SteadyState::settleFunc )
- );
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation "
+ "only if the object has not yet been initialized.",
+ new OpFunc0< SteadyState >( &SteadyState::settleFunc )
+ );
static DestFinfo resettle( "resettle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation ",
- new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
- );
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation ",
+ new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
+ );
static DestFinfo showMatrices( "showMatrices",
- "Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices",
- new OpFunc0< SteadyState >( &SteadyState::showMatrices )
- );
+ "Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices",
+ new OpFunc0< SteadyState >( &SteadyState::showMatrices )
+ );
static DestFinfo randomInit( "randomInit",
- "Generate random initial conditions consistent with the mass"
- "conservation rules. Typically invoked in order to scan"
- "states",
- new EpFunc0< SteadyState >(
- &SteadyState::randomizeInitialCondition )
- );
+ "Generate random initial conditions consistent with the mass"
+ "conservation rules. Typically invoked in order to scan"
+ "states",
+ new EpFunc0< SteadyState >(
+ &SteadyState::randomizeInitialCondition )
+ );
///////////////////////////////////////////////////////
// Shared definitions
///////////////////////////////////////////////////////
static Finfo * steadyStateFinfos[] =
{
- &stoich, // Value
- &badStoichiometry, // ReadOnlyValue
- &isInitialized, // ReadOnlyValue
- &nIter, // ReadOnlyValue
- &status, // ReadOnlyValue
- &maxIter, // Value
- &convergenceCriterion, // ReadOnlyValue
- &numVarPools, // ReadOnlyValue
- &rank, // ReadOnlyValue
- &stateType, // ReadOnlyValue
- &nNegEigenvalues, // ReadOnlyValue
- &nPosEigenvalues, // ReadOnlyValue
- &solutionStatus, // ReadOnlyValue
- &total, // LookupValue
- &eigenvalues, // ReadOnlyLookupValue
- &setupMatrix, // DestFinfo
- &settle, // DestFinfo
- &resettle, // DestFinfo
- &showMatrices, // DestFinfo
- &randomInit, // DestFinfo
+ &stoich, // Value
+ &badStoichiometry, // ReadOnlyValue
+ &isInitialized, // ReadOnlyValue
+ &nIter, // ReadOnlyValue
+ &status, // ReadOnlyValue
+ &maxIter, // Value
+ &convergenceCriterion, // ReadOnlyValue
+ &numVarPools, // ReadOnlyValue
+ &rank, // ReadOnlyValue
+ &stateType, // ReadOnlyValue
+ &nNegEigenvalues, // ReadOnlyValue
+ &nPosEigenvalues, // ReadOnlyValue
+ &solutionStatus, // ReadOnlyValue
+ &total, // LookupValue
+ &eigenvalues, // ReadOnlyLookupValue
+ &setupMatrix, // DestFinfo
+ &settle, // DestFinfo
+ &resettle, // DestFinfo
+ &showMatrices, // DestFinfo
+ &randomInit, // DestFinfo
};
@@ -278,7 +257,7 @@ const Cinfo* SteadyState::initCinfo()
"Note that the method finds unstable as well as stable fixed "
"points.\n "
"The SteadyState class also provides a utility function "
- "*randomInit()* to "
+ "*randomInit()* to "
"randomly initialize the concentrations, within the constraints "
"of stoichiometry. This is useful if you are trying to find "
"the major fixed points of the system. Note that this is "
@@ -368,12 +347,10 @@ void SteadyState::setStoich( Id value )
numVarPools_ = Field< unsigned int >::get( stoich_, "numVarPools" );
nReacs_ = Field< unsigned int >::get( stoich_, "numRates" );
setupSSmatrix();
- double vol = LookupField< unsigned int, double >::get(
- stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
+ double vol = LookupField< unsigned int, double >::get(stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
pool_.setVolume( vol );
pool_.setStoich( stoichPtr, 0 );
- pool_.updateAllRateTerms( stoichPtr->getRateTerms(),
- stoichPtr->getNumCoreRates() );
+ pool_.updateAllRateTerms( stoichPtr->getRateTerms(), stoichPtr->getNumCoreRates() );
isInitialized_ = 1;
}
@@ -513,9 +490,9 @@ void SteadyState::showMatrices()
return;
}
int numConsv = numVarPools_ - rank_;
- cout << "Totals: ";
+ cout << "Totals: ";
for ( int i = 0; i < numConsv; ++i )
- cout << total_[i] << " ";
+ cout << total_[i] << " ";
cout << endl;
cout << "gamma " << gamma_ << endl;
cout << "Nr " << Nr_ << endl;
@@ -549,9 +526,7 @@ void SteadyState::setupSSmatrix()
{
double x = 0;
if ( j == colIndex[k] && k < rowStart[i+1] )
- {
x = entry[k++];
- }
N(i,j) = x;
LU_(i,j) = x;
}
@@ -714,7 +689,7 @@ static bool isSolutionValid( const vector< double >& x )
for( size_t i = 0; i < x.size(); i++ )
{
double v = x[i];
- if ( std::isnan( v ) or std::isinf( v ) )
+ if ( std::isnan( v ) || std::isinf( v ) )
{
cout << "Warning: SteadyState iteration gave nan/inf concs\n";
return false;
diff --git a/moose-core/ksolve/SteadyStateGsl.cpp b/moose-core/ksolve/SteadyStateGsl.cpp
index 295b5256..5aa0941d 100644
--- a/moose-core/ksolve/SteadyStateGsl.cpp
+++ b/moose-core/ksolve/SteadyStateGsl.cpp
@@ -87,20 +87,20 @@ const Cinfo* SteadyState::initCinfo()
* This picks up the entire Stoich data structure
static Finfo* gslShared[] =
{
- new SrcFinfo( "reinitSrc", Ftype0::global() ),
- new DestFinfo( "assignStoich",
- Ftype1< void* >::global(),
- RFCAST( &SteadyState::assignStoichFunc )
- ),
- new DestFinfo( "setMolN",
- Ftype2< double, unsigned int >::global(),
- RFCAST( &SteadyState::setMolN )
- ),
- new SrcFinfo( "requestYsrc", Ftype0::global() ),
- new DestFinfo( "assignY",
- Ftype1< double* >::global(),
- RFCAST( &SteadyState::assignY )
- ),
+ new SrcFinfo( "reinitSrc", Ftype0::global() ),
+ new DestFinfo( "assignStoich",
+ Ftype1< void* >::global(),
+ RFCAST( &SteadyState::assignStoichFunc )
+ ),
+ new DestFinfo( "setMolN",
+ Ftype2< double, unsigned int >::global(),
+ RFCAST( &SteadyState::setMolN )
+ ),
+ new SrcFinfo( "requestYsrc", Ftype0::global() ),
+ new DestFinfo( "assignY",
+ Ftype1< double* >::global(),
+ RFCAST( &SteadyState::assignY )
+ ),
};
*/
@@ -205,61 +205,61 @@ const Cinfo* SteadyState::initCinfo()
// MsgDest definitions
///////////////////////////////////////////////////////
static DestFinfo setupMatrix( "setupMatrix",
- "This function initializes and rebuilds the matrices used "
- "in the calculation.",
- new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
- );
+ "This function initializes and rebuilds the matrices used "
+ "in the calculation.",
+ new OpFunc0< SteadyState >(&SteadyState::setupMatrix)
+ );
static DestFinfo settle( "settle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation "
- "only if the object has not yet been initialized.",
- new OpFunc0< SteadyState >( &SteadyState::settleFunc )
- );
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation "
+ "only if the object has not yet been initialized.",
+ new OpFunc0< SteadyState >( &SteadyState::settleFunc )
+ );
static DestFinfo resettle( "resettle",
- "Finds the nearest steady state to the current initial "
- "conditions. This function rebuilds the entire calculation ",
- new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
- );
+ "Finds the nearest steady state to the current initial "
+ "conditions. This function rebuilds the entire calculation ",
+ new OpFunc0< SteadyState >( &SteadyState::resettleFunc )
+ );
static DestFinfo showMatrices( "showMatrices",
- "Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices",
- new OpFunc0< SteadyState >( &SteadyState::showMatrices )
- );
+ "Utility function to show the matrices derived for the "
+ "calculations on the reaction system. Shows the Nr, gamma, and total matrices",
+ new OpFunc0< SteadyState >( &SteadyState::showMatrices )
+ );
static DestFinfo randomInit( "randomInit",
- "Generate random initial conditions consistent with the mass"
- "conservation rules. Typically invoked in order to scan"
- "states",
- new EpFunc0< SteadyState >(
- &SteadyState::randomizeInitialCondition )
- );
+ "Generate random initial conditions consistent with the mass"
+ "conservation rules. Typically invoked in order to scan"
+ "states",
+ new EpFunc0< SteadyState >(
+ &SteadyState::randomizeInitialCondition )
+ );
+
///////////////////////////////////////////////////////
// Shared definitions
///////////////////////////////////////////////////////
static Finfo * steadyStateFinfos[] =
{
- &stoich, // Value
- &badStoichiometry, // ReadOnlyValue
- &isInitialized, // ReadOnlyValue
- &nIter, // ReadOnlyValue
- &status, // ReadOnlyValue
- &maxIter, // Value
- &convergenceCriterion, // ReadOnlyValue
- &numVarPools, // ReadOnlyValue
- &rank, // ReadOnlyValue
- &stateType, // ReadOnlyValue
- &nNegEigenvalues, // ReadOnlyValue
- &nPosEigenvalues, // ReadOnlyValue
- &solutionStatus, // ReadOnlyValue
- &total, // LookupValue
- &eigenvalues, // ReadOnlyLookupValue
- &setupMatrix, // DestFinfo
- &settle, // DestFinfo
- &resettle, // DestFinfo
- &showMatrices, // DestFinfo
- &randomInit, // DestFinfo
-
-
+ &stoich, // Value
+ &badStoichiometry, // ReadOnlyValue
+ &isInitialized, // ReadOnlyValue
+ &nIter, // ReadOnlyValue
+ &status, // ReadOnlyValue
+ &maxIter, // Value
+ &convergenceCriterion, // ReadOnlyValue
+ &numVarPools, // ReadOnlyValue
+ &rank, // ReadOnlyValue
+ &stateType, // ReadOnlyValue
+ &nNegEigenvalues, // ReadOnlyValue
+ &nPosEigenvalues, // ReadOnlyValue
+ &solutionStatus, // ReadOnlyValue
+ &total, // LookupValue
+ &eigenvalues, // ReadOnlyLookupValue
+ &setupMatrix, // DestFinfo
+ &settle, // DestFinfo
+ &resettle, // DestFinfo
+ &showMatrices, // DestFinfo
+ &randomInit, // DestFinfo
};
static string doc[] =
@@ -276,7 +276,7 @@ const Cinfo* SteadyState::initCinfo()
"Note that the method finds unstable as well as stable fixed "
"points.\n "
"The SteadyState class also provides a utility function "
- "*randomInit()* to "
+ "*randomInit()* to "
"randomly initialize the concentrations, within the constraints "
"of stoichiometry. This is useful if you are trying to find "
"the major fixed points of the system. Note that this is "
@@ -316,7 +316,6 @@ static const Cinfo* steadyStateCinfo = SteadyState::initCinfo();
///////////////////////////////////////////////////
// Class function definitions
///////////////////////////////////////////////////
-
SteadyState::SteadyState()
:
nIter_( 0 ),
@@ -382,9 +381,10 @@ void SteadyState::setStoich( Id value )
double vol = LookupField< unsigned int, double >::get(
stoichPtr->getCompartment(), "oneVoxelVolume", 0 );
pool_.setVolume( vol );
- pool_.setStoich( stoichPtr, 0 );
- pool_.updateAllRateTerms( stoichPtr->getRateTerms(),
- stoichPtr->getNumCoreRates() );
+
+ pool_.setStoich( stoichPtr, nullptr );
+
+ pool_.updateAllRateTerms( stoichPtr->getRateTerms(), stoichPtr->getNumCoreRates() );
isInitialized_ = 1;
}
@@ -548,9 +548,9 @@ void SteadyState::showMatrices()
return;
}
int numConsv = numVarPools_ - rank_;
- cout << "Totals: ";
+ cout << "Totals: ";
for ( int i = 0; i < numConsv; ++i )
- cout << total_[i] << " ";
+ cout << total_[i] << " ";
cout << endl;
#ifdef USE_GSL
print_gsl_mat( gamma_, "gamma" );
@@ -584,7 +584,7 @@ void SteadyState::setupSSmatrix()
{
gsl_matrix_set (LU_, i, i + nReacs_, 1 );
unsigned int k = rowStart[i];
- // cout << endl << i << ": ";
+ // cout << endl << i << ": ";
for ( unsigned int j = 0; j < nReacs_; ++j )
{
double x = 0;
@@ -592,7 +592,7 @@ void SteadyState::setupSSmatrix()
{
x = entry[k++];
}
- // cout << " " << x;
+ // cout << " " << x;
gsl_matrix_set (N, i, j, x);
gsl_matrix_set (LU_, i, j, x );
}
@@ -637,10 +637,10 @@ void SteadyState::setupSSmatrix()
/*
cout << "S = (";
for ( unsigned int j = 0; j < numVarPools_; ++j )
- cout << s_->S()[ j ] << ", ";
+ cout << s_->S()[ j ] << ", ";
cout << "), Sinit = ( ";
for ( unsigned int j = 0; j < numVarPools_; ++j )
- cout << s_->Sinit()[ j ] << ", ";
+ cout << s_->Sinit()[ j ] << ", ";
cout << ")\n";
*/
Id ksolve = Field< Id >::get( stoich_, "ksolve" );
diff --git a/moose-core/ksolve/VoxelPools.cpp b/moose-core/ksolve/VoxelPools.cpp
index ea575304..25e8ac7e 100644
--- a/moose-core/ksolve/VoxelPools.cpp
+++ b/moose-core/ksolve/VoxelPools.cpp
@@ -6,7 +6,8 @@
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
-#include "header.h"
+
+#include "../basecode/header.h"
#ifdef USE_GSL
#include <gsl/gsl_errno.h>
@@ -66,9 +67,12 @@ void VoxelPools::reinit( double dt )
void VoxelPools::setStoich( Stoich* s, const OdeSystem* ode )
{
stoichPtr_ = s;
- absTol_ = ode->epsAbs;
- relTol_ = ode->epsRel;
- method_ = ode->method;
+ if( ode )
+ {
+ epsAbs_ = ode->epsAbs;
+ epsRel_ = ode->epsRel;
+ method_ = ode->method;
+ }
#ifdef USE_GSL
if ( ode )
@@ -77,10 +81,9 @@ void VoxelPools::setStoich( Stoich* s, const OdeSystem* ode )
if ( driver_ )
gsl_odeiv2_driver_free( driver_ );
- driver_ = gsl_odeiv2_driver_alloc_y_new(
- &sys_, ode->gslStep, ode->initStepSize,
- ode->epsAbs, ode->epsRel
- );
+ driver_ = gsl_odeiv2_driver_alloc_y_new( &sys_, ode->gslStep
+ , ode->initStepSize, ode->epsAbs, ode->epsRel
+ );
}
#endif
VoxelPoolsBase::reinit();
@@ -89,6 +92,7 @@ void VoxelPools::setStoich( Stoich* s, const OdeSystem* ode )
void VoxelPools::advance( const ProcInfo* p )
{
double t = p->currTime - p->dt;
+
#ifdef USE_GSL
int status = gsl_odeiv2_driver_apply( driver_, &t, p->currTime, varS());
if ( status != GSL_SUCCESS )
@@ -135,114 +139,41 @@ void VoxelPools::advance( const ProcInfo* p )
* user should provide the stepping size when using fixed dt. This feature
* can be incredibly useful on large system.
*/
- const double fixedDt = 0.1;
- if( method_ == "rk2" )
+ // Variout stepper times are listed here:
+ // https://www.boost.org/doc/libs/1_68_0/libs/numeric/odeint/doc/html/boost_numeric_odeint/odeint_in_detail/steppers.html#boost_numeric_odeint.odeint_in_detail.steppers.explicit_steppers
+
+ auto sys = [this](const vector_type_& dy, vector_type_& dydt, const double t) {
+ VoxelPools::evalRates(this, dy, dydt); };
+
+ // This is usually the default method for boost: Runge Kutta Fehlberg
+ if( method_ == "rk5")
+ odeint::integrate_const( rk_karp_stepper_type_()
+ , sys , Svec() , p->currTime - p->dt, p->currTime, p->dt);
+ else if( method_ == "rk2" )
odeint::integrate_const( rk_midpoint_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if( method_ == "rk4" )
odeint::integrate_const( rk4_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
- else if( method_ == "rk5")
- odeint::integrate_const( rk_karp_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt );
else if( method_ == "rk5a")
- odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol_, relTol_ )
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::integrate_adaptive( odeint::make_controlled<rk_dopri_stepper_type_>( epsAbs_, epsRel_ )
+ , sys , Svec() , p->currTime - p->dt , p->currTime, p->dt );
else if ("rk54" == method_ )
odeint::integrate_const( rk_karp_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys , Svec() , p->currTime - p->dt, p->currTime, p->dt);
else if ("rk54a" == method_ )
- odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol_, relTol_ )
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
- else if ("rk5" == method_ )
- odeint::integrate_const( rk_dopri_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , std::min( p->dt, fixedDt )
- );
- else if ("rk5a" == method_ )
- odeint::integrate_adaptive(
- odeint::make_controlled<rk_dopri_stepper_type_>( absTol_, relTol_ )
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::integrate_adaptive( odeint::make_controlled<rk_karp_stepper_type_>( epsAbs_, epsRel_ )
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if( method_ == "rk8" )
odeint::integrate_const( rk_felhberg_stepper_type_()
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt, p->currTime, std::min( p->dt, fixedDt )
- );
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else if( method_ == "rk8a" )
- odeint::integrate_adaptive(
- odeint::make_controlled<rk_felhberg_stepper_type_>( absTol_, relTol_ )
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
-
+ odeint::integrate_adaptive( odeint::make_controlled<rk_felhberg_stepper_type_>( epsAbs_, epsRel_ )
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
else
- odeint::integrate_adaptive(
- odeint::make_controlled<rk_karp_stepper_type_>( absTol_, relTol_ )
- , [this](const vector_type_& dy, vector_type_& dydt, const double t) {
- VoxelPools::evalRates(this, dy, dydt );
- }
- , Svec()
- , p->currTime - p->dt
- , p->currTime
- , p->dt
- );
+ odeint::integrate_adaptive( odeint::make_controlled<rk_karp_stepper_type_>( epsAbs_, epsRel_ )
+ , sys, Svec(), p->currTime - p->dt, p->currTime, p->dt);
#endif
if ( !stoichPtr_->getAllowNegative() ) // clean out negatives
@@ -353,8 +284,7 @@ void VoxelPools::updateRates( const double* s, double* yprime ) const
stoichPtr_->getNumProxyPools();
// totVar should include proxyPools if this voxel does not use them
unsigned int totInvar = stoichPtr_->getNumBufPools();
- assert( N.nColumns() == 0 ||
- N.nRows() == stoichPtr_->getNumAllPools() );
+ assert( N.nColumns() == 0 || N.nRows() == stoichPtr_->getNumAllPools() );
assert( N.nColumns() == rates_.size() );
for ( vector< RateTerm* >::const_iterator
diff --git a/moose-core/ksolve/VoxelPools.h b/moose-core/ksolve/VoxelPools.h
index a39b151c..04c5bb8c 100644
--- a/moose-core/ksolve/VoxelPools.h
+++ b/moose-core/ksolve/VoxelPools.h
@@ -99,8 +99,8 @@ private:
gsl_odeiv2_system sys_;
#endif
- double absTol_;
- double relTol_;
+ double epsAbs_;
+ double epsRel_;
string method_;
};
diff --git a/moose-core/python/rdesigneur/rdesigneur.py b/moose-core/python/rdesigneur/rdesigneur.py
index 568bac94..447faa11 100644
--- a/moose-core/python/rdesigneur/rdesigneur.py
+++ b/moose-core/python/rdesigneur/rdesigneur.py
@@ -73,6 +73,7 @@ class rdesigneur:
combineSegments = True,
stealCellFromLibrary = False,
verbose = True,
+ benchmark = False,
addSomaChemCompt = False, # Put a soma chemCompt on neuroMesh
addEndoChemCompt = False, # Put an endo compartment, typically for ER, on each of the NeuroMesh compartments.
diffusionLength= 2e-6,
@@ -96,8 +97,8 @@ class rdesigneur:
chemDistrib = [],
adaptorList= [],
stimList = [],
- plotList = [],
- moogList = [],
+ plotList = [], # elecpath, geom_expr, object, field, title ['wave' [min max]]
+ moogList = [],
params = None
):
""" Constructor of the rdesigner. This just sets up internal fields
@@ -110,6 +111,7 @@ class rdesigneur:
self.combineSegments = combineSegments
self.stealCellFromLibrary = stealCellFromLibrary
self.verbose = verbose
+ self.benchmark = benchmark
self.addSomaChemCompt = addSomaChemCompt
self.addEndoChemCompt = addEndoChemCompt
self.diffusionLength= diffusionLength
@@ -138,11 +140,16 @@ class rdesigneur:
self.params = params
self.adaptorList = adaptorList
- self.stimList = stimList
- self.plotList = plotList
- self.saveList = plotList #ADDED BY Sarthak
+ try:
+ self.stimList = [ rstim.convertArg(i) for i in stimList ]
+ self.plotList = [ rplot.convertArg(i) for i in plotList ]
+ self.moogList = [ rmoog.convertArg(i) for i in moogList ]
+ except BuildError as msg:
+ print("Error: rdesigneur: " + msg)
+ quit()
+
+ #self.saveList = plotList #ADDED BY Sarthak
self.saveAs = []
- self.moogList = moogList
self.plotNames = []
self.wavePlotNames = []
self.saveNames = []
@@ -166,7 +173,9 @@ class rdesigneur:
################################################################
def _printModelStats( self ):
- print("\n\tRdesigneur: Elec model has",
+ if not self.verbose:
+ return
+ print("\nRdesigneur: Elec model has",
self.elecid.numCompartments, "compartments and",
self.elecid.numSpines, "spines on",
len( self.cellPortionElist ), "compartments.")
@@ -184,17 +193,15 @@ class rdesigneur:
return
self.model = moose.Neutral( modelPath )
self.modelPath = modelPath
- print( "[INFO ] rdesigneur: Building model. " )
funcs = [ self.installCellFromProtos, self.buildPassiveDistrib
, self.buildChanDistrib, self.buildSpineDistrib, self.buildChemDistrib
, self._configureSolvers, self.buildAdaptors, self._buildStims
, self._buildPlots, self._buildMoogli, self._configureHSolve
- , self._configureClocks, self._printModelStats, self._savePlots
+ , self._configureClocks, self._printModelStats
]
for i, _func in enumerate( funcs ):
- if self.verbose:
+ if self.benchmark:
print( " + (%d/%d) executing %25s"%(i, len(funcs), _func.__name__), end=' ' )
- sys.stdout.flush()
t0 = time.time()
try:
_func( )
@@ -203,11 +210,12 @@ class rdesigneur:
moose.delete( self.model )
return
t = time.time() - t0
- if self.verbose:
+ if self.benchmark:
msg = r' ... DONE'
if t > 1:
msg += ' %.3f sec' % t
print( msg )
+ sys.stdout.flush()
def installCellFromProtos( self ):
if self.stealCellFromLibrary:
@@ -463,10 +471,10 @@ class rdesigneur:
# Here we hack geomExpr to use it for the syn weight. We assume it
# is just a number. In due course
# it should be possible to actually evaluate it according to geom.
- synWeight = float( stimInfo[1] )
+ synWeight = float( stimInfo.geom_expr )
stimObj = []
for i in dendCompts + spineCompts:
- path = i.path + '/' + stimInfo[2] + '/sh/synapse[0]'
+ path = i.path + '/' + stimInfo.relpath + '/sh/synapse[0]'
if moose.exists( path ):
synInput = make_synInput( name='synInput', parent=path )
synInput.doPeriodic = doPeriodic
@@ -486,6 +494,10 @@ class rdesigneur:
# Expression can use p, g, L, len, dia, maxP, maxG, maxL.
temp = []
for i in self.passiveDistrib:
+ if (len( i ) < 3) or (len(i) %2 != 1):
+ raise BuildError( "buildPassiveDistrib: Need 3 + N*2 arguments, have {}".format( len(i) ) )
+
+ temp.append( '.' )
temp.extend( i )
temp.extend( [""] )
self.elecid.passiveDistribution = temp
@@ -608,18 +620,17 @@ class rdesigneur:
# [ region_wildcard, region_expr, path, field, title]
def _parseComptField( self, comptList, plotSpec, knownFields ):
# Put in stuff to go through fields if the target is a chem object
- field = plotSpec[3]
+ field = plotSpec.field
if not field in knownFields:
print("Warning: Rdesigneur::_parseComptField: Unknown field '{}'".format( field ) )
return (), ""
kf = knownFields[field] # Find the field to decide type.
if kf[0] in ['CaConcBase', 'ChanBase', 'NMDAChan', 'VClamp']:
- objList = self._collapseElistToPathAndClass( comptList, plotSpec[2], kf[0] )
+ objList = self._collapseElistToPathAndClass( comptList, plotSpec.relpath, kf[0] )
return objList, kf[1]
-
elif field in [ 'n', 'conc', 'volume']:
- path = plotSpec[2]
+ path = plotSpec.relpath
pos = path.find( '/' )
if pos == -1: # Assume it is in the dend compartment.
path = 'dend/' + path
@@ -640,13 +651,13 @@ class rdesigneur:
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] )
+ allObj = moose.vec( self.modelPath + '/chem/' + plotSpec.relpath )
#print "####### allObj=", self.modelPath + '/chem/' + plotSpec[2]
if len( allObj ) >= len( voxelVec ):
objList = [ allObj[int(j)] for j in voxelVec]
else:
objList = []
- print( "Warn: Rdesigneur::_parseComptField: unknown Object: '%s'" % plotSpec[2] )
+ print( "Warning: Rdesigneur::_parseComptField: unknown Object: '", plotSpec.relpath, "'" )
#print "############", chemCompt, len(objList), kf[1]
return objList, kf[1]
@@ -678,7 +689,7 @@ class rdesigneur:
dummy = moose.element( '/' )
k = 0
for i in self.plotList:
- pair = i[0] + " " + i[1]
+ pair = i.elecpath + ' ' + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
@@ -686,26 +697,26 @@ class rdesigneur:
assert( plotField == plotField2 )
plotObj3 = plotObj + plotObj2
numPlots = sum( q != dummy for q in plotObj3 )
- if numPlots == 0:
- return
-
- tabname = graphs.path + '/plot' + str(k)
- scale = knownFields[i[3]][2]
- units = knownFields[i[3]][3]
- ymin = i[6] if len(i) > 7 else 0
- ymax = i[7] if len(i) > 7 else 0
- if len( i ) > 5 and i[5] == 'wave':
- self.wavePlotNames.append( [ tabname, i[4], k, scale, units, i[3], ymin, ymax ] )
- else:
- self.plotNames.append( [ tabname, i[4], k, scale, units, i[3], ymin, ymax ] )
- k += 1
- if i[3] in [ 'n', 'conc', 'volume', 'Gbar' ]:
- tabs = moose.Table2( tabname, numPlots )
- else:
- tabs = moose.Table( tabname, numPlots )
- if i[3] == 'spikeTime':
- tabs.vec.threshold = -0.02 # Threshold for classifying Vm as a spike.
- tabs.vec.useSpikeMode = True # spike detect mode on
+ #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.field][2]
+ units = knownFields[i.field][3]
+ if i.mode == 'wave':
+ self.wavePlotNames.append( [ tabname, i.title, k, scale, units, i ] )
+ else:
+ self.plotNames.append( [ tabname, i.title, k, scale, units, i.field, i.ymin, i.ymax ] )
+ if len( i.saveFile ) > 4 and i.saveFile[-4] == '.xml' or i.saveFile:
+ self.saveNames.append( [ tabname, len(self.saveNames), scale, units, i ] )
+
+ k += 1
+ if i.field == 'n' or i.field == 'conc' or i.field == 'volume' or i.field == 'Gbar':
+ tabs = moose.Table2( tabname, numPlots )
+ else:
+ tabs = moose.Table( tabname, numPlots )
+ if i.field == 'spikeTime':
+ tabs.vec.threshold = -0.02 # Threshold for classifying Vm as a spike.
+ tabs.vec.useSpikeMode = True # spike detect mode on
vtabs = moose.vec( tabs )
q = 0
@@ -731,8 +742,8 @@ class rdesigneur:
moogliBase = moose.Neutral( self.modelPath + '/moogli' )
k = 0
for i in self.moogList:
- kf = knownFields[i[3]]
- pair = i[0] + " " + i[1]
+ kf = knownFields[i.field]
+ pair = i.elecpath + " " + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
dendObj, mooField = self._parseComptField( dendCompts, i, knownFields )
@@ -740,13 +751,6 @@ class rdesigneur:
assert( mooField == mooField2 )
mooObj3 = dendObj + spineObj
numMoogli = len( mooObj3 )
- #dendComptMap = self.dendCompt.elecComptMap
- #self.moogliViewer = rmoogli.makeMoogli( self, mooObj3, mooField )
- if len( i ) == 5:
- i.extend( kf[4:6] )
- elif len( i ) == 6:
- i.extend( [kf[5]] )
- #self.moogliViewer = rmoogli.makeMoogli( self, mooObj3, i, kf )
self.moogNames.append( rmoogli.makeMoogli( self, mooObj3, i, kf ) )
@@ -815,10 +819,15 @@ rdesigneur.rmoogli.updateMoogliViewer()
plt.title( i[1] )
plt.xlabel( "position (voxels)" )
plt.ylabel( i[4] )
- mn = np.min(vpts)
- mx = np.max(vpts)
- if mn/mx < 0.3:
- mn = 0
+ plotinfo = i[5]
+ if plotinfo.ymin == plotinfo.ymax:
+ mn = np.min(vpts)
+ mx = np.max(vpts)
+ if mn/mx < 0.3:
+ mn = 0
+ else:
+ mn = plotinfo.ymin
+ mx = plotinfo.ymax
ax.set_ylim( mn, mx )
line, = plt.plot( range( len( vtab ) ), vpts[0] )
timeLabel = plt.text( len(vtab ) * 0.05, mn + 0.9*(mx-mn), 'time = 0' )
@@ -847,134 +856,13 @@ rdesigneur.rmoogli.updateMoogliViewer()
Email address: sarthaks442@gmail.com
Heavily modified by U.S. Bhalla
'''
-
- def _savePlots( self ):
- if self.verbose:
- print( 'rdesigneur: Saving plots ...', end = ' ' )
- sys.stdout.flush()
-
- knownFields = {
- 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
- 'Cm':('CompartmentBase', 'getCm', 1e12, 'Memb. capacitance (pF)' ),
- 'Rm':('CompartmentBase', 'getRm', 1e-9, 'Memb. Res (GOhm)' ),
- 'Ra':('CompartmentBase', 'getRa', 1e-6, 'Axial Res (MOhm)' ),
- 'spikeTime':('CompartmentBase', 'getVm', 1, 'Spike Times (s)'),
- 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
- 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
- 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
- 'modulation':('ChanBase', 'getModulation', 1, 'chan modulation (unitless)' ),
- 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
- 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
- 'ICa':('NMDAChan', 'getICa', 1e9, 'Ca current (nA)' ),
- 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
- 'n':('PoolBase', 'getN', 1, '# of molecules'),
- 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' ),
- 'volume':('PoolBase', 'getVolume', 1e18, 'Volume (um^3)' ),
- 'current':('VClamp', 'getCurrent', 1e9, 'Holding Current (nA)')
- }
-
- save_graphs = moose.Neutral( self.modelPath + '/save_graphs' )
- dummy = moose.element( '/' )
- k = 0
-
- for i in self.saveList:
- pair = i[0] + " " + i[1]
- dendCompts = self.elecid.compartmentsFromExpression[ pair ]
- spineCompts = self.elecid.spinesFromExpression[ pair ]
- plotObj, plotField = self._parseComptField( dendCompts, i, knownFields )
- plotObj2, plotField2 = self._parseComptField( spineCompts, i, knownFields )
- assert( plotField == plotField2 )
- plotObj3 = plotObj + plotObj2
- numPlots = sum( i != dummy for i in plotObj3 )
- if numPlots > 0:
- save_tabname = save_graphs.path + '/save_plot' + str(k)
- scale = knownFields[i[3]][2]
- units = knownFields[i[3]][3]
- self.saveNames.append( ( save_tabname, i[4], k, scale, units ) )
- k += 1
- if i[3] in [ 'n', 'conc', 'volume', 'Gbar' ]:
- save_tabs = moose.Table2( save_tabname, numPlots )
- save_vtabs = moose.vec( save_tabs )
- else:
- save_tabs = moose.Table( save_tabname, numPlots )
- save_vtabs = moose.vec( save_tabs )
- if i[3] == 'spikeTime':
- save_vtabs.threshold = -0.02 # Threshold for classifying Vm as a spike.
- save_vtabs.useSpikeMode = True # spike detect mode on
- q = 0
- for p in [ x for x in plotObj3 if x != dummy ]:
- moose.connect( save_vtabs[q], 'requestOut', p, plotField )
- q += 1
-
- if self.verbose:
- print( ' ... DONE.' )
-
- def _getTimeSeriesTable( self ):
-
- '''
- This function gets the list with all the details of the simulation
- required for plotting.
- This function adds flexibility in terms of the details
- we wish to store.
- '''
-
- knownFields = {
- 'Vm':('CompartmentBase', 'getVm', 1000, 'Memb. Potential (mV)' ),
- 'spikeTime':('CompartmentBase', 'getVm', 1, 'Spike Times (s)'),
- 'Im':('CompartmentBase', 'getIm', 1e9, 'Memb. current (nA)' ),
- 'inject':('CompartmentBase', 'getInject', 1e9, 'inject current (nA)' ),
- 'Gbar':('ChanBase', 'getGbar', 1e9, 'chan max conductance (nS)' ),
- 'Gk':('ChanBase', 'getGk', 1e9, 'chan conductance (nS)' ),
- 'Ik':('ChanBase', 'getIk', 1e9, 'chan current (nA)' ),
- 'ICa':('NMDAChan', 'getICa', 1e9, 'Ca current (nA)' ),
- 'Ca':('CaConcBase', 'getCa', 1e3, 'Ca conc (uM)' ),
- 'n':('PoolBase', 'getN', 1, '# of molecules'),
- 'conc':('PoolBase', 'getConc', 1000, 'Concentration (uM)' ),
- 'volume':('PoolBase', 'getVolume', 1e18, 'Volume (um^3)' )
- }
-
- '''
- This takes data from plotList
- saveList is exactly like plotList but with a few additional arguments:
- ->It will have a resolution option, i.e., the number of decimal figures to which the value should be rounded
- ->There is a list of "saveAs" formats
- With saveList, the user will able to set what all details he wishes to be saved.
- '''
-
- for i,ind in enumerate(self.saveNames):
- pair = self.saveList[i][0] + " " + self.saveList[i][1]
- dendCompts = self.elecid.compartmentsFromExpression[ pair ]
- spineCompts = self.elecid.spinesFromExpression[ pair ]
- # Here we get the object details from plotList
- savePlotObj, plotField = self._parseComptField( dendCompts, self.saveList[i], knownFields )
- savePlotObj2, plotField2 = self._parseComptField( spineCompts, self.saveList[i], knownFields )
- savePlotObj3 = savePlotObj + savePlotObj2
-
- rowList = list(ind)
- save_vtab = moose.vec( ind[0] )
- t = np.arange( 0, save_vtab[0].vector.size, 1 ) * save_vtab[0].dt
-
- rowList.append(save_vtab[0].dt)
- rowList.append(t)
- rowList.append([jvec.vector * ind[3] for jvec in save_vtab]) #get values
- rowList.append(self.saveList[i][3])
- rowList.append(filter(lambda obj: obj.path != '/', savePlotObj3)) #this filters out dummy elements
-
- if (type(self.saveList[i][-1])==int):
- rowList.append(self.saveList[i][-1])
- else:
- rowList.append(12)
-
- self.tabForXML.append(rowList)
- rowList = []
-
- timeSeriesTable = self.tabForXML # the list with all the details of plot
- return timeSeriesTable
-
- def _writeXML( self, filename, timeSeriesData ): #to write to XML file
-
- plotData = timeSeriesData
- print("[CAUTION] The '%s' file might be very large if all the compartments are to be saved." % filename)
+ def _writeXML( self, plotData, time, vtab ):
+ tabname = plotData[0]
+ idx = plotData[1]
+ scale = plotData[2]
+ units = plotData[3]
+ rp = plotData[4]
+ filename = rp.saveFile[:-4] + str(idx) + '.xml'
root = etree.Element("TimeSeriesPlot")
parameters = etree.SubElement( root, "parameters" )
if self.params == None:
@@ -987,36 +875,33 @@ rdesigneur.rmoogli.updateMoogliViewer()
#plotData contains all the details of a single plot
title = etree.SubElement( root, "timeSeries" )
- title.set( 'title', str(plotData[1]))
- title.set( 'field', str(plotData[8]))
- title.set( 'scale', str(plotData[3]))
- title.set( 'units', str(plotData[4]))
- title.set( 'dt', str(plotData[5]))
+ title.set( 'title', rp.title)
+ title.set( 'field', rp.field)
+ title.set( 'scale', str(scale) )
+ title.set( 'units', units)
+ title.set( 'dt', str(vtab[0].dt) )
+ res = rp.saveResolution
p = []
- assert(len(plotData[7]) == len(plotData[9]))
-
- res = plotData[10]
- for ind, jvec in enumerate(plotData[7]):
+ for t, v in zip( time, vtab ):
p.append( etree.SubElement( title, "data"))
- p[-1].set( 'path', str(plotData[9][ind].path))
- p[-1].text = ''.join( str(round(value,res)) + ' ' for value in jvec )
+ p[-1].set( 'path', v.path )
+ p[-1].text = ''.join( str(round(y,res)) + ' ' for y in v.vector )
tree = etree.ElementTree(root)
tree.write(filename)
- def _writeCSV(self, filename, timeSeriesData):
-
- plotData = timeSeriesData
- dataList = []
- header = []
- time = plotData[6]
- res = plotData[10]
-
- for ind, jvec in enumerate(plotData[7]):
- header.append(plotData[9][ind].path)
- dataList.append([round(value,res) for value in jvec.tolist()])
- dl = [tuple(lst) for lst in dataList]
- rows = zip(tuple(time), *dl)
- header.insert(0, "time")
+ def _writeCSV( self, plotData, time, vtab ):
+ tabname = plotData[0]
+ idx = plotData[1]
+ scale = plotData[2]
+ units = plotData[3]
+ rp = plotData[4]
+ filename = rp.saveFile[:-4] + str(idx) + '.csv'
+
+ header = ["time",]
+ valMatrix = [time,]
+ header.extend( [ v.path for v in vtab ] )
+ valMatrix.extend( [ v.vector for v in vtab ] )
+ nv = np.array( valMatrix ).T
with open(filename, 'wb') as f:
writer = csv.writer(f, quoting=csv.QUOTE_MINIMAL)
writer.writerow(header)
@@ -1024,42 +909,25 @@ rdesigneur.rmoogli.updateMoogliViewer()
writer.writerow(row)
##########****SAVING*****###############
- def _saveFormats(self, timeSeriesData, k, *filenames):
- "This takes in the filenames and writes to corresponding format."
- if filenames:
- for filename in filenames:
- for name in filename:
- print (name)
- if name[-4:] == '.xml':
- self._writeXML(name, timeSeriesData)
- print(name, " written")
- elif name[-4:] == '.csv':
- self._writeCSV(name, timeSeriesData)
- print(name, " written")
- else:
- print("Save format not known")
- pass
- else:
- pass
def _save( self ):
- timeSeriesTable = self._getTimeSeriesTable()
- for i,sList in enumerate(self.saveList):
-
- if (len(sList) >= 6) and (type(sList[5]) != int):
- self.saveAs.extend(filter(lambda fmt: type(fmt)!=int, sList[5:]))
- try:
- timeSeriesData = timeSeriesTable[i]
- except IndexError:
- print("The object to be plotted has all dummy elements.")
- pass
- self._saveFormats(timeSeriesData, i, self.saveAs)
- self.saveAs=[]
+ for i in self.saveNames:
+ tabname = i[0]
+ idx = i[1]
+ scale = i[2]
+ units = i[3]
+ rp = i[4] # The rplot data structure, it has the setup info.
+
+ vtab = moose.vec( tabname )
+ t = np.arange( 0, vtab[0].vector.size, 1 ) * vtab[0].dt
+ ftype = rp.filename[-4:]
+ if ftype == '.xml':
+ self._writeXML( i, t, vtab )
+ elif ftype == '.csv':
+ self._writeCSV( i, t, vtab )
else:
- pass
- else:
- pass
+ print("Save format '{}' not known, please use .csv or .xml".format( ftype ) )
################################################################
# Here we set up the stims
@@ -1080,17 +948,17 @@ rdesigneur.rmoogli.updateMoogliViewer()
k = 0
# Stimlist = [path, geomExpr, relPath, field, expr_string]
for i in self.stimList:
- pair = i[0] + " " + i[1]
+ pair = i.elecpath + " " + i.geom_expr
dendCompts = self.elecid.compartmentsFromExpression[ pair ]
spineCompts = self.elecid.spinesFromExpression[ pair ]
#print( "pair = {}, numcompts = {},{} ".format( pair, len( dendCompts), len( spineCompts ) ) )
- if i[3] == 'vclamp':
+ if i.field == 'vclamp':
stimObj3 = self._buildVclampOnCompt( dendCompts, spineCompts, i )
stimField = 'commandIn'
- elif i[3] == 'randsyn':
+ elif i.field == 'randsyn':
stimObj3 = self._buildSynInputOnCompt( dendCompts, spineCompts, i )
stimField = 'setRate'
- elif i[3] == 'periodicsyn':
+ elif i.field == 'periodicsyn':
stimObj3 = self._buildSynInputOnCompt( dendCompts, spineCompts, i, doPeriodic = True )
stimField = 'setRate'
else:
@@ -1103,7 +971,7 @@ rdesigneur.rmoogli.updateMoogliViewer()
funcname = stims.path + '/stim' + str(k)
k += 1
func = moose.Function( funcname )
- func.expr = i[4]
+ func.expr = i.expr
#if i[3] == 'vclamp': # Hack to clean up initial condition
func.doEvalAtReinit = 1
for q in stimObj3:
@@ -1619,3 +1487,95 @@ rdesigneur.rmoogli.updateMoogliViewer()
for j in range( i[1], i[2] ):
moose.connect( i[3], 'requestOut', chemVec[j], chemFieldSrc)
msg = moose.connect( i[3], 'output', elObj, elecFieldDest )
+
+
+#######################################################################
+# Some helper classes, used to define argument lists.
+#######################################################################
+
+class baseplot:
+ def __init__( self,
+ elecpath='soma', geom_expr='1', relpath='.', field='Vm' ):
+ self.elecpath = elecpath
+ self.geom_expr = geom_expr
+ self.relpath = relpath
+ self.field = field
+
+class rplot( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'Vm',
+ title = 'Membrane potential',
+ mode = 'time',
+ ymin = 0.0, ymax = 0.0,
+ saveFile = "", saveResolution = 3, show = True ):
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.title = title
+ self.mode = mode # Options: time, wave, wave_still, raster
+ self.ymin = ymin # If ymin == ymax, it autoscales.
+ self.ymax = ymax
+ if len( saveFile ) < 5:
+ self.saveFile = ""
+ else:
+ f = saveFile.split('.')
+ if len(f) < 2 or ( f[-1] != 'xml' and f[-1] != 'csv' ):
+ raise BuildError( "rplot: Filetype is '{}', must be of type .xml or .csv.".format( f[-1] ) )
+ self.saveFile = saveFile
+ self.show = show
+
+ def printme( self ):
+ print( "{}, {}, {}, {}, {}, {}, {}, {}, {}, {}".format(
+ self.elecpath,
+ self.geom_expr, self.relpath, self.field, self.title,
+ self.mode, self.ymin, self.ymax, self.saveFile, self.show ) )
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rplot ):
+ return arg
+ elif isinstance( arg, list ):
+ return rplot( *arg )
+ else:
+ raise BuildError( "rplot initialization failed" )
+
+class rmoog( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'Vm',
+ title = 'Membrane potential',
+ ymin = 0.0, ymax = 0.0,
+ show = True ): # Could put in other display options.
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.title = title
+ self.ymin = ymin # If ymin == ymax, it autoscales.
+ self.ymax = ymax
+ self.show = show
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rmoog ):
+ return arg
+ elif isinstance( arg, list ):
+ return rmoog( *arg )
+ else:
+ raise BuildError( "rmoog initialization failed" )
+
+ # Stimlist = [path, geomExpr, relPath, field, expr_string]
+class rstim( baseplot ):
+ def __init__( self,
+ elecpath = 'soma', geom_expr = '1', relpath = '.', field = 'inject', expr = '0'):
+ baseplot.__init__( self, elecpath, geom_expr, relpath, field )
+ self.expr = expr
+
+ def printme( self ):
+ print( "{}, {}, {}, {}, {}, {}, {}, {}, {}, {}".format(
+ self.elecpath,
+ self.geom_expr, self.relpath, self.field, self.expr ) )
+
+ @staticmethod
+ def convertArg( arg ):
+ if isinstance( arg, rstim ):
+ return arg
+ elif isinstance( arg, list ):
+ return rstim( *arg )
+ else:
+ raise BuildError( "rstim initialization failed" )
+
diff --git a/moose-core/python/rdesigneur/rmoogli.py b/moose-core/python/rdesigneur/rmoogli.py
index 16317b56..f673dad7 100644
--- a/moose-core/python/rdesigneur/rmoogli.py
+++ b/moose-core/python/rdesigneur/rmoogli.py
@@ -29,7 +29,7 @@ def makeMoogli( rd, mooObj, args, fieldInfo ):
else:
ymin = fieldInfo[4]
ymax = fieldInfo[5]
- print( "fieldinfo = {}, ymin = {}, ymax = {}".format( fieldInfo, ymin, ymax ))
+ #print( "fieldinfo = {}, ymin = {}, ymax = {}".format( fieldInfo, ymin, ymax ))
viewer = moogul.MooView()
if mooField == 'n' or mooField == 'conc':
diff --git a/moose-core/tests/python/chem_models/19085.cspace b/moose-core/tests/python/chem_models/19085.cspace
new file mode 100644
index 00000000..1d2cf355
--- /dev/null
+++ b/moose-core/tests/python/chem_models/19085.cspace
@@ -0,0 +1 @@
+M101: |DabX|Jbca| 5.59269 0.0157641 0.172865 0.361005 4.72728 1.08558 0.0982933
\ No newline at end of file
diff --git a/moose-core/tests/python/testdisabled_dose_response.py b/moose-core/tests/python/testdisabled_dose_response.py
new file mode 100644
index 00000000..a840565a
--- /dev/null
+++ b/moose-core/tests/python/testdisabled_dose_response.py
@@ -0,0 +1,106 @@
+# -*- coding: utf-8 -*-
+## Makes and plots the dose response curve for bistable models
+## Author: Sahil Moza
+## June 26, 2014
+## Update:
+## Friday 14 September 2018 05:48:42 PM IST
+## Tunrned into a light-weight test by Dilawar Singh
+
+import os
+import sys
+import moose
+import numpy as np
+
+sdir_ = os.path.dirname( os.path.realpath( __file__ ) )
+
+def setupSteadyState(simdt,plotDt):
+
+ ksolve = moose.Ksolve( '/model/kinetics/ksolve' )
+ stoich = moose.Stoich( '/model/kinetics/stoich' )
+ stoich.compartment = moose.element('/model/kinetics')
+ stoich.ksolve = ksolve
+ stoich.path = "/model/kinetics/##"
+ state = moose.SteadyState( '/model/kinetics/state' )
+ moose.reinit()
+ state.stoich = stoich
+ state.showMatrices()
+ state.convergenceCriterion = 1e-8
+ return ksolve, state
+
+def parseModelName(fileName):
+ pos1=fileName.rfind('/')
+ pos2=fileName.rfind('.')
+ directory=fileName[:pos1]
+ prefix=fileName[pos1+1:pos2]
+ suffix=fileName[pos2+1:len(fileName)]
+ return directory, prefix, suffix
+
+# Solve for the steady state
+def getState( ksolve, state, vol):
+ scale = 1.0 / ( vol * 6.022e23 )
+ moose.reinit()
+ state.randomInit() # Removing random initial condition to systematically make Dose reponse curves.
+ moose.start( 2.0 ) # Run the model for 2 seconds.
+ state.settle()
+
+ vector = []
+ a = moose.element( '/model/kinetics/a' ).conc
+ for x in ksolve.nVec[0]:
+ vector.append( x * scale)
+ failedSteadyState = any([np.isnan(x) for x in vector])
+ if not (failedSteadyState):
+ return state.stateType, state.solutionStatus, a, vector
+
+
+def main():
+ # Setup parameters for simulation and plotting
+ simdt= 1e-2
+ plotDt= 1
+
+ # Factors to change in the dose concentration in log scale
+ factorExponent = 10 ## Base: ten raised to some power.
+ factorBegin = -10
+ factorEnd = 11
+ factorStepsize = 2
+ factorScale = 10.0 ## To scale up or down the factors
+
+ # Load Model and set up the steady state solver.
+ # model = sys.argv[1] # To load model from a file.
+ model = os.path.join( sdir_, 'chem_models/19085.cspace' )
+ modelPath, modelName, modelType = parseModelName(model)
+ outputDir = modelPath
+
+ modelId = moose.loadModel(model, 'model', 'ee')
+ dosePath = '/model/kinetics/b/DabX' # The dose entity
+
+ ksolve, state = setupSteadyState( simdt, plotDt)
+ vol = moose.element( '/model/kinetics' ).volume
+ iterInit = 100
+ solutionVector = []
+ factorArr = []
+
+ enz = moose.element(dosePath)
+ init = float(enz.kcat) # Dose parameter
+
+ # Change Dose here to .
+ for factor in range(factorBegin, factorEnd, factorStepsize ):
+ scale = factorExponent ** (factor/factorScale)
+ enz.kcat = init * scale
+ print( "scale={:.3f}\tkcat={:.3f}".format( scale, enz.kcat) )
+ for num in range(iterInit):
+ stateType, solStatus, a, vector = getState( ksolve, state, vol)
+ if solStatus == 0:
+ #solutionVector.append(vector[0]/sum(vector))
+ solutionVector.append(a)
+ factorArr.append(scale)
+
+ joint = np.array([factorArr, solutionVector])
+ joint = joint[:,joint[1,:].argsort()]
+ got = np.mean( joint ), np.std( joint )
+ expected = (1.2247, 2.46)
+ # Close upto 2 decimal place is good enough.
+ assert np.isclose(got, expected, atol=1e-2).all(), "Got %s, expected %s" % (got, expected)
+ print( joint )
+
+if __name__ == '__main__':
+ main()
diff --git a/moose-examples/.travis.yml b/moose-examples/.travis.yml
index 0f209164..46cb8a38 100644
--- a/moose-examples/.travis.yml
+++ b/moose-examples/.travis.yml
@@ -1,4 +1,9 @@
sudo : required
+language: python
+python:
+ - "2.7"
+ - "3.6"
+ - "3.7"
notifications:
email:
@@ -7,16 +12,8 @@ notifications:
- bhalla@ncbs.res.in
- hrani@ncbs.res.in
-install:
- - sudo ./.travis_prepare.sh
-
script:
+ - pip install pymoose --user --pre
- ./.travis_run.sh
exclude: [vendor]
-
-deploy:
- provider: pages
- skip-cleanup: true
- github-token: $GHI_TOKEN #
- keep-history: true
diff --git a/moose-examples/.travis_prepare.sh b/moose-examples/.travis_prepare.sh
deleted file mode 100755
index a2ad83cc..00000000
--- a/moose-examples/.travis_prepare.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/usr/bin/env bash
-# ROOT should run this script.
-VERSION=$(lsb_release -r | cut -f2)
-apt-get -y update
-apt-get install cmake coreutils --force-yes
-apt-get -y --force-yes install python-qt4 python-pip graphviz
-apt-get -y --force-yes install python-h5py python-scipy python-pygraphviz
-wget -nv https://download.opensuse.org/repositories/home:moose/xUbuntu_$VERSION/Release.key -O Release.key
-apt-key add - < Release.key
-cat <<EOF > /etc/apt/sources.list.d/home:moose.list
-deb http://download.opensuse.org/repositories/home:/moose/xUbuntu_${VERSION}/ /
-EOF
-apt-get update
-apt-get install python-numpy python-matplotlib python-networkx
-apt-get install pymoose
-python -m pip install python-libsbml --user
diff --git a/moose-examples/neuroml2/NML2_SingleCompHHCell.nml b/moose-examples/neuroml2/NML2_SingleCompHHCell.nml
new file mode 100644
index 00000000..1b1d43b9
--- /dev/null
+++ b/moose-examples/neuroml2/NML2_SingleCompHHCell.nml
@@ -0,0 +1,90 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
+ id="NML2_SingleCompHHCell">
+
+ <!-- Single compartment cell with HH channels -->
+
+ <!-- This is a "pure" NeuroML 2 file. It can be included in a LEMS file for use in a simulaton
+ by the LEMS interpreter, see LEMS_NML2_Ex5_DetCell.xml -->
+
+ <ionChannelHH id="passiveChan" conductance="10pS">
+ <notes>Leak conductance</notes>
+ </ionChannelHH>
+
+
+ <ionChannelHH id="naChan" conductance="10pS" species="na">
+ <notes>Na channel</notes>
+
+ <gateHHrates id="m" instances="3">
+ <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
+ <reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
+ </gateHHrates>
+
+ <gateHHrates id="h" instances="1">
+ <forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
+ <reverseRate type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
+ </gateHHrates>
+
+ </ionChannelHH>
+
+
+ <ionChannelHH id="kChan" conductance="10pS" species="k">
+
+ <gateHHrates id="n" instances="4">
+ <forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
+ <reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
+ </gateHHrates>
+
+ </ionChannelHH>
+
+
+
+ <cell id="hhcell">
+
+ <morphology id="morph1">
+ <segment id="0" name="soma">
+ <proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 um^2-->
+ <distal x="0" y="0" z="0" diameter="17.841242"/>
+ </segment>
+
+ <segmentGroup id="soma_group">
+ <member segment="0"/>
+ </segmentGroup>
+
+ </morphology>
+
+ <biophysicalProperties id="bioPhys1">
+
+ <membraneProperties>
+
+ <channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV" ion="non_specific"/>
+ <channelDensity id="naChans" ionChannel="naChan" condDensity="120.0 mS_per_cm2" erev="50.0 mV" ion="na"/>
+ <channelDensity id="kChans" ionChannel="kChan" condDensity="360 S_per_m2" erev="-77mV" ion="k"/>
+
+ <spikeThresh value="-20mV"/>
+ <specificCapacitance value="1.0 uF_per_cm2"/>
+ <initMembPotential value="-65mV"/>
+
+ </membraneProperties>
+
+ <intracellularProperties>
+ <resistivity value="0.03 kohm_cm"/> <!-- Note: not used in single compartment simulations -->
+ </intracellularProperties>
+
+ </biophysicalProperties>
+
+ </cell>
+
+ <pulseGenerator id="pulseGen1" delay="100ms" duration="100ms" amplitude="0.08nA"/>
+
+
+ <network id="net1">
+ <population id="hhpop" component="hhcell" size="1"/>
+ <explicitInput target="hhpop[0]" input="pulseGen1"/>
+ </network>
+
+</neuroml>
+
diff --git a/moose-examples/neuroml2/converter.py b/moose-examples/neuroml2/converter.py
new file mode 100644
index 00000000..0aec54f3
--- /dev/null
+++ b/moose-examples/neuroml2/converter.py
@@ -0,0 +1,209 @@
+# -*- coding: utf-8 -*-
+# converter.py ---
+#
+# Filename: mtoneuroml.py
+# Description:
+# Author:
+# Maintainer:
+# Created: Mon Apr 22 12:15:23 2013 (+0530)
+# Version:
+# Last-Updated: Wed Jul 10 16:36:14 2013 (+0530)
+# By: subha
+# Update #: 819
+# URL:
+# Keywords:
+# Compatibility:
+#
+#
+
+# Commentary:
+#
+# Utility for converting a MOOSE model into NeuroML2. This uses Python
+# libNeuroML.
+#
+#
+
+# Change log:
+#
+# Tue May 21 16:58:03 IST 2013 - Subha moved the code for function
+# fitting to hhfit.py.
+
+#
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 3, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; see the file COPYING. If not, write to
+# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
+# Floor, Boston, MA 02110-1301, USA.
+#
+#
+
+# Code:
+
+#!!!!! TODO: unit conversion !!!!
+
+try:
+ from future_builtins import zip
+except ImportError:
+ pass
+import traceback
+import warnings
+from collections import deque
+import numpy as np
+from scipy.optimize import curve_fit
+from matplotlib import pyplot as plt
+
+import moose
+from moose.utils import autoposition
+import neuroml
+import hhfit
+
+
+def convert_morphology(root, positions='auto'):
+ """Convert moose neuron morphology contained under `root` into a
+ NeuroML object. The id of the return object is
+ {root.name}_morphology. Each segment object gets the numeric value
+ of the moose id of the object. The name of the segments are same
+ as the corresponding moose compartment.
+
+ Parameters
+ ----------
+ root : a moose element containing a single cell model.
+
+ positions : string
+ flag to indicate if the positions of the end points of the
+ compartments are explicitly available in the compartments or
+ should be automatically generated. Possible values:
+
+ `auto` - automatically generate z coordinates using length of the
+ compartments.
+
+ `explicit` - model has explicit coordinates for all compartments.
+
+ Return
+ ------
+ a neuroml.Morphology instance.
+
+ """
+ if positions == 'auto':
+ queue = deque([autoposition(root)])
+ elif positions == 'explicit':
+ compartments = moose.wildcardFind('%s/##[TYPE=Compartment]' % (root.path))
+ queue = deque([compartment for compartment in map(moose.element, compartments)
+ if len(compartment.neighbours['axial']) == 0])
+ if len(queue) != 1:
+ raise Exception('There must be one and only one top level compartment. Found %d' % (len(topcomp_list)))
+ else:
+ raise Exception('allowed values for keyword argument positions=`auto` or `explicit`')
+ comp_seg = {}
+ parent = None
+ while len(queue) > 0:
+ compartment = queue.popleft()
+ proximal = neuroml.Point3DWithDiam(x=compartment.x0,
+ y=compartment.y0,
+ z=compartment.z0,
+ diameter=compartment.diameter)
+ distal = neuroml.Point3DWithDiam(x=compartment.x,
+ y=compartment.y,
+ z=compartment.z,
+ diameter=compartment.diameter)
+ plist = list(map(moose.element, compartment.neighbours['axial']))
+ try:
+ parent = neuroml.SegmentParent(segments=comp_seg[moose.element(plist[0])].id)
+ except (KeyError, IndexError) as e:
+ parent = None
+ segment = neuroml.Segment(id=compartment.id_.value,
+ proximal=proximal,
+ distal=distal,
+ parent=parent)
+ # TODO: For the time being using numerical value of the moose
+ # id for neuroml id.This needs to be updated for handling
+ # array elements
+ segment.name = compartment.name
+ comp_seg[compartment] = segment
+ queue.extend([comp for comp in map(moose.element, compartment.neighbours['raxial'])])
+ morph = neuroml.Morphology(id='%s_morphology' % (root.name))
+ morph.segments.extend(comp_seg.values())
+ return morph
+
+
+def define_vdep_rate(fn, name):
+ """Define new component type with generic expressions for voltage
+ dependent rate.
+
+ """
+ ctype = neuroml.ComponentType(name)
+ # This is going to be ugly ...
+
+
+
+def convert_hhgate(gate):
+ """Convert a MOOSE gate into GateHHRates in NeuroML"""
+ hh_rates = neuroml.GateHHRates(id=gate.id_.value, name=gate.name)
+ alpha = gate.tableA.copy()
+ beta = gate.tableB - alpha
+ vrange = np.linspace(gate.min, gate.max, len(alpha))
+ afn, ap = hhfit.find_ratefn(vrange, alpha)
+ bfn, bp = hhfit.find_ratefn(vrange, beta)
+ if afn is None:
+ raise Exception('could not find a fitting function for `alpha`')
+ if bfn is None:
+ raise Exception('could not find a fitting function for `alpha`')
+ afn_type = fn_rate_map[afn]
+ afn_component_type = None
+ if afn_type is None:
+ afn_type, afn_component_type = define_component_type(afn)
+ hh_rates.forward_rate = neuroml.HHRate(type=afn_type,
+ midpoint='%gmV' % (ap[2]),
+ scale='%gmV' % (ap[1]),
+ rate='%gper_ms' % (ap[0]))
+ bfn_type = fn_rate_map[bfn]
+ bfn_component_type = None
+ if bfn_type is None:
+ bfn_type, bfn_component_type = define_component_type(bfn)
+ hh_rates.reverse_rate = neuroml.HHRate(type=bfn_type,
+ midpoint='%gmV' % (bp[2]),
+ scale='%gmV' % (bp[1]),
+ rate='%gper_ms' % (bp[0]))
+ return hh_rates, afn_component_type, bfn_component_type
+
+
+def convert_hhchannel(channel):
+ """Convert a moose HHChannel object into a neuroml element.
+
+ TODO: need to check useConcentration option for Ca2+ and V
+ dependent gates. How to handle generic expressions???
+
+ """
+ nml_channel = neuroml.IonChannel(id=channel.id_.value
+ , name=channel.name, type='ionChannelHH'
+ , conductance=channel.Gbar
+ )
+ if channel.Xpower > 0:
+ hh_rate_x = convert_hhgate(channel.gateX[0])
+ hh_rate_x.instances = channel.Xpower
+ nml_channel.gate.append(hh_rate_x)
+
+ if channel.Ypower > 0:
+ hh_rate_y = convert_hhgate(channel.gateY[0])
+ hh_rate_y.instances = channel.Ypower
+ nml_channel.gate.append(hh_rate_y)
+
+ if channel.Zpower > 0:
+ hh_rate_z = convert_hhgate(channel.gateZ[0])
+ hh_rate_y.instances = channel.Zpower
+ nml_channel.gate.append(hh_rate_z)
+ return nml_channel
+
+
+#
+# converter.py ends here
diff --git a/moose-examples/neuroml2/passiveCell.nml b/moose-examples/neuroml2/passiveCell.nml
new file mode 100644
index 00000000..9b91f253
--- /dev/null
+++ b/moose-examples/neuroml2/passiveCell.nml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
+ id="NML2_SingleCompHHCell">
+
+
+ <ionChannel type="ionChannelPassive" id="passiveChan" conductance="10pS">
+ <notes>Leak conductance</notes>
+ </ionChannel>
+
+ <cell id="passiveCell">
+
+ <morphology id="morph1">
+ <segment id="0" name="soma">
+ <proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 ?m�-->
+ <distal x="0" y="0" z="0" diameter="17.841242"/>
+ </segment>
+
+ <segmentGroup id="soma_group">
+ <member segment="0"/>
+ </segmentGroup>
+
+ </morphology>
+
+ <biophysicalProperties id="bioPhys1">
+
+ <membraneProperties>
+ <channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0S_per_m2" erev="-54.3mV" ion="non_specific"/>
+ <spikeThresh value="-20mV"/>
+ <specificCapacitance value="1.0uF_per_cm2"/>
+ <initMembPotential value="-66.6mV"/>
+ </membraneProperties>
+
+ <intracellularProperties>
+ <resistivity value="0.03kohm_cm"/> <!-- Note: not used in single compartment simulations -->
+ </intracellularProperties>
+
+ </biophysicalProperties>
+
+ </cell>
+
+ <pulseGenerator id="pulseGen1" delay="50ms" duration="50ms" amplitude="0.08nA"/>
+
+
+ <network id="net1">
+ <population id="pop0" component="passiveCell" size="1"/>
+ <explicitInput target="pop0[0]" input="pulseGen1"/>
+ </network>
+
+</neuroml>
diff --git a/moose-examples/neuroml2/run_cell.py b/moose-examples/neuroml2/run_cell.py
new file mode 100644
index 00000000..174358d0
--- /dev/null
+++ b/moose-examples/neuroml2/run_cell.py
@@ -0,0 +1,112 @@
+# -*- coding: utf-8 -*-
+# run_cell.py ---
+#
+# Filename: run_cell.py
+# Description:
+# Author:
+# Maintainer: P Gleeson
+# Version:
+# URL:
+# Keywords:
+# Compatibility:
+#
+#
+
+# Commentary:
+#
+#
+#
+#
+
+# Change log:
+# Sunday 16 September 2018 10:04:24 AM IST
+# - Tweaked file to to make it compatible with moose.
+#
+#
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 3, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; see the file COPYING. If not, write to
+# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
+# Floor, Boston, MA 02110-1301, USA.
+#
+#
+
+# Code:
+
+import moose
+import sys
+import numpy as np
+
+
+def run(nogui):
+
+ filename = 'passiveCell.nml'
+ print('Loading: %s'%filename)
+ reader = moose.mooseReadNML2( filename )
+ assert reader
+ reader.read(filename)
+
+ msoma = reader.getComp(reader.doc.networks[0].populations[0].id,0,0)
+ print(msoma)
+
+
+ data = moose.Neutral('/data')
+
+ pg = reader.getInput('pulseGen1')
+
+ inj = moose.Table('%s/pulse' % (data.path))
+ moose.connect(inj, 'requestOut', pg, 'getOutputValue')
+
+
+ vm = moose.Table('%s/Vm' % (data.path))
+ moose.connect(vm, 'requestOut', msoma, 'getVm')
+
+ simdt = 1e-6
+ plotdt = 1e-4
+ simtime = 150e-3
+
+ if (1):
+ #moose.showmsg( '/clock' )
+ for i in range(8):
+ moose.setClock( i, simdt )
+ moose.setClock( 8, plotdt )
+ moose.reinit()
+ else:
+ utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
+ moose.showmsg( '/clock' )
+
+ moose.start(simtime)
+
+ print("Finished simulation!")
+
+ t = np.linspace(0, simtime, len(vm.vector))
+
+ if not nogui:
+ import matplotlib.pyplot as plt
+
+ plt.subplot(211)
+ plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
+ plt.legend()
+ plt.title('Vm')
+ plt.subplot(212)
+ plt.title('Input')
+ plt.plot(t, inj.vector * 1e9, label='injected (nA)')
+ #plt.plot(t, gK.vector * 1e6, label='K')
+ #plt.plot(t, gNa.vector * 1e6, label='Na')
+ plt.legend()
+ plt.show()
+ plt.close()
+
+if __name__ == '__main__':
+ nogui = '-nogui' in sys.argv
+ run(nogui)
diff --git a/moose-examples/neuroml2/run_hhcell.py b/moose-examples/neuroml2/run_hhcell.py
new file mode 100644
index 00000000..2b38cd67
--- /dev/null
+++ b/moose-examples/neuroml2/run_hhcell.py
@@ -0,0 +1,151 @@
+# -*- coding: utf-8 -*-
+# run_hhcell.py ---
+#
+# Filename: run_hhcell.py
+# Description:
+# Author:
+# Maintainer: P Gleeson
+# Version:
+# URL:
+# Keywords:
+# Compatibility:
+#
+#
+
+# Commentary:
+#
+#
+#
+#
+
+# Change log:
+#
+#
+#
+#
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 3, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; see the file COPYING. If not, write to
+# the Free Software Foundation, Inc., 51 Franklin Street, Fifth
+# Floor, Boston, MA 02110-1301, USA.
+#
+#
+
+# Code:
+
+import moose
+import sys
+import numpy as np
+
+def test_channel_gates():
+ """Creates prototype channels under `/library` and plots the time
+ constants (tau) and activation (minf, hinf, ninf) parameters for the
+ channel gates.
+
+ """
+ import matplotlib.pyplot as plt
+ lib = moose.Neutral('/library')
+ m = moose.element('/library[0]/naChan[0]/gateX')
+ h = moose.element('/library[0]/naChan[0]/gateY')
+ n = moose.element('/library[0]/kChan[0]/gateX')
+ v = np.linspace(n.min,n.max, n.divs+1)
+
+ plt.subplot(221)
+ plt.plot(v, 1/m.tableB, label='tau_m')
+ plt.plot(v, 1/h.tableB, label='tau_h')
+ plt.plot(v, 1/n.tableB, label='tau_n')
+ plt.legend()
+
+ plt.subplot(222)
+ plt.plot(v, m.tableA/m.tableB, label='m_inf')
+ plt.plot(v, h.tableA/h.tableB, label='h_inf')
+ plt.plot(v, n.tableA/n.tableB, label='n_inf')
+ plt.legend()
+
+ plt.subplot(223)
+ plt.plot(v, m.tableA, label='mA(alpha)')
+ plt.plot(v, h.tableA, label='hA(alpha)')
+ plt.plot(v, n.tableA, label='nA(alpha)')
+ plt.legend()
+ plt.subplot(224)
+
+ plt.plot(v, m.tableB, label='mB')
+ plt.plot(v, m.tableB-m.tableA, label='mB-A(beta)')
+
+ plt.plot(v, h.tableB, label='hB')
+ plt.plot(v, h.tableB-h.tableA, label='hB-A(beta)')
+
+ plt.plot(v, n.tableB, label='nB')
+ plt.plot(v, n.tableB-n.tableA, label='nB-nA(beta)')
+ plt.legend()
+
+ plt.show()
+
+
+def run(nogui):
+ filename = 'NML2_SingleCompHHCell.nml'
+ print('Loading: %s'%filename)
+ reader = moose.mooseReadNML2(filename)
+ msoma = reader.getComp(reader.doc.networks[0].populations[0].id,0,0)
+ print(msoma)
+ data = moose.Neutral('/data')
+ pg = reader.getInput('pulseGen1')
+ inj = moose.Table('%s/pulse' % (data.path))
+ moose.connect(inj, 'requestOut', pg, 'getOutputValue')
+ vm = moose.Table('%s/Vm' % (data.path))
+ moose.connect(vm, 'requestOut', msoma, 'getVm')
+
+ simdt = 1e-6
+ plotdt = 1e-4
+ simtime = 300e-3
+ if (1):
+ #moose.showmsg( '/clock' )
+ for i in range(8):
+ moose.setClock( i, simdt )
+ moose.setClock( 8, plotdt )
+ moose.reinit()
+ else:
+ utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
+ moose.showmsg( '/clock' )
+ moose.start(simtime)
+
+ print("Finished simulation!")
+
+ t = np.linspace(0, simtime, len(vm.vector))
+
+ if not nogui:
+ import matplotlib.pyplot as plt
+
+ vfile = open('moose_v_hh.dat','w')
+
+ for i in range(len(t)):
+ vfile.write('%s\t%s\n'%(t[i],vm.vector[i]))
+ vfile.close()
+ plt.subplot(211)
+ plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
+ plt.legend()
+ plt.title('Vm')
+ plt.subplot(212)
+ plt.title('Input')
+ plt.plot(t, inj.vector * 1e9, label='injected (nA)')
+ #plt.plot(t, gK.vector * 1e6, label='K')
+ #plt.plot(t, gNa.vector * 1e6, label='Na')
+ plt.legend()
+ plt.figure()
+ test_channel_gates()
+ plt.show()
+ plt.close()
+
+
+if __name__ == '__main__':
+ nogui = '-nogui' in sys.argv
+ run(nogui)
diff --git a/moose-examples/squid/squid.py b/moose-examples/squid/squid.py
index dae8ff9d..de3efc46 100644
--- a/moose-examples/squid/squid.py
+++ b/moose-examples/squid/squid.py
@@ -28,8 +28,6 @@
# Code:
import sys
-sys.path.append('../../python')
-
import numpy
import moose
@@ -99,22 +97,24 @@ class IonChannel(moose.HHChannel):
def alpha_m(self):
if self.Xpower == 0:
return numpy.array([])
- return numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableA)
+ return numpy.array(moose.element('%s/gateX' % (self.path)).tableA)
@property
def beta_m(self):
if self.Xpower == 0:
return numpy.array([])
- return numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableB) - numpy.array(moose.HHGate('%s/gateX' % (self.path)).tableA)
+ return numpy.array(moose.element('%s/gateX' % (self.path)).tableB) - \
+ numpy.array(moose.element('%s/gateX' % (self.path)).tableA)
@property
def alpha_h(self):
if self.Ypower == 0:
return numpy.array([])
- return numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableA)
+ return numpy.array(moose.element('%s/gateY' % (self.path)).tableA)
@property
def beta_h(self):
if self.Ypower == 0:
return numpy.array([])
- return numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableB) - numpy.array(moose.HHGate('%s/gateY' % (self.path)).tableA)
+ return numpy.array(moose.element('%s/gateY' % (self.path)).tableB) \
+ - numpy.array(moose.element('%s/gateY' % (self.path)).tableA)
class SquidAxon(moose.Compartment):
EREST_ACT = 0.0 # can be -70 mV if not following original HH convention
diff --git a/moose-examples/squid/squid_demo.py b/moose-examples/squid/squid_demo.py
index d243b0f5..d87d615c 100644
--- a/moose-examples/squid/squid_demo.py
+++ b/moose-examples/squid/squid_demo.py
@@ -1,5 +1,4 @@
-
- # -*- coding: utf-8 -*-
+# -*- coding: utf-8 -*-
# squidgui.py ---
#
# Filename: squidgui.py
@@ -48,18 +47,21 @@
# Code:
import sys
-sys.path.append('../../python')
import os
-os.environ['NUMPTHREADS'] = '1'
-
from collections import defaultdict
import time
-from PyQt4 import QtGui
-from PyQt4 import QtCore
+pyqt_ver_ = 4
+try:
+ from PyQt5 import QtGui, QtCore
+ pyqt_ver_ = 5
+except ImportError as e:
+ from PyQt4 import QtGui
+ from PyQt4 import QtCore
import numpy
from matplotlib.figure import Figure
-from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas, NavigationToolbar2QT as NavigationToolbar
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
import moose
@@ -163,7 +165,6 @@ def set_default_line_edit_size(widget):
widget.setMinimumSize(default_line_edit_size)
widget.setMaximumSize(default_line_edit_size)
-
class SquidGui(QtGui.QMainWindow):
defaults = {}
defaults.update(SquidAxon.defaults)
diff --git a/moose-examples/squid/squid_demo_qt5.py b/moose-examples/squid/squid_demo_qt5.py
new file mode 100644
index 00000000..59979883
--- /dev/null
+++ b/moose-examples/squid/squid_demo_qt5.py
@@ -0,0 +1,861 @@
+# -*- coding: utf-8 -*-
+# Description: Squid Model
+# Author: Subha
+# Maintainer: Dilawar Singh <dilawars@ncbs.res.in>
+# Created: Mon Jul 9 18:23:55 2012 (+0530)
+# Version:
+# Last-Updated: Wednesday 12 September 2018 04:23:52 PM IST
+# PyQt5 version
+
+import sys
+import os
+from collections import defaultdict
+import time
+
+from PyQt5 import QtGui, QtCore
+from PyQt5.QtWidgets import QMainWindow, QApplication, QGroupBox, QSizePolicy
+from PyQt5.QtWidgets import QLabel, QLineEdit, QGridLayout, QDockWidget
+from PyQt5.QtWidgets import QCheckBox, QTabWidget, QComboBox, QWidget
+from PyQt5.QtWidgets import QVBoxLayout, QFrame, QHBoxLayout, QAction
+from PyQt5.QtWidgets import QToolButton, QScrollArea, QTextBrowser
+
+import numpy
+from matplotlib.figure import Figure
+from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
+
+import moose
+
+from squid import *
+from squid_setup import SquidSetup
+from electronics import ClampCircuit
+
+
+tooltip_Nernst = """<h3>Ionic equilibrium potential</h3>
+<p/>
+The equilibrium potential for ion C is given by Nernst equation:
+<p>
+E<sub>C</sub> = (RT/zF) * ln([C]<sub>out</sub> / [C]<sub>in</sub>)
+</p>
+where R is the ideal gas constant (8.3145 J/mol K),<br>
+ T is absolute temperature,<br>
+ z is the valence of the ion,<br>
+ F is Faraday's constant 96480 C/mol,<br>
+ [C]<sub>out</sub> is concentration of C outside the membrane,<br>
+ [C]<sub>in</sub> is concentration of C inside the membrane."""
+
+tooltip_Erest = """<h3>Resting membrane potential</h3>
+<p/>
+The resting membrane potential is determined by the ionic
+concentrations inside and outside the cell membrane and is given by
+the Goldman-Hodgkin-Katz equation:
+<p>
+
+V = (RT/F) * ln((P<sub>K</sub>[K<sup>+</sup>]<sub>out</sub> + P<sub>Na</sub>[Na<sup>+</sup>]<sub>out</sub> + P<sub>Cl</sub>[Cl<sup>-</sup>]<sub>in</sub>) / (P<sub>K</sub>[K<sup>+</sup>]in + P<sub>Na</sub>[Na<sup>+</sup>]<sub>in</sub> + P<sub>Cl</sub>[Cl<sup>-</sup>]<sub>out</sub>))
+
+</p>
+where P<sub>C</sub> is the permeability of the membrane to ion C.
+
+"""
+
+tooltip_NaChan = """<h3>Na+ channel conductance</h3>
+<p/>
+The Na<sup>+</sup> channel conductance in squid giant axon is given by:
+
+<p> G<sub>Na</sub> = GÌ„<sub>Na</sub> * m<sup>3</sup> * h </p>
+
+and the current through this channel is:
+<p>
+I<sub>Na</sub> = G<sub>Na</sub> * (V - E<sub>Na</sub>) = GÌ„<sub>Na</sub> * m<sup>3</sup> * h * (V - E<sub>Na</sub>)
+</p>
+
+where GÌ„<sub>Na</sub> is the peak conductance of Na<sup>+</sup> channel, m is
+the fraction of activation gates open and h is the fraction of
+deactivation gates open. The transition from open to closed state has
+first order kinetics:
+<p> dm/dt = α<sub>m</sub> * ( 1 - m) - β<sub>m</sub> * m </p>
+and similarly for h.
+
+The steady state values are:
+<p> m<sub>∞</sub> = α<sub>m</sub>/(α<sub>m</sub> + β<sub>m</sub>) </p>
+and time constant for steady state is:
+<p>τ<sub>m</sub> = 1/ (α<sub>m</sub> + β<sub>m</sub>) </p>
+and similarly for h.
+"""
+
+tooltip_KChan = """<h3>K+ channel conductance</h3>
+<p/>The K+ channel conductance in squid giant axon is given by:
+
+<p> G<sub>K</sub> = GÌ„<sub>K</sub> * n<sup>4</sup></p>
+
+and the current through this channel is:
+<p>
+I<sub>K</sub> = G<sub>K</sub> * (V - E<sub>K</sub>) = GÌ„<sub>K</sub> * n<sup>4</sup> * (V - E<sub>K</sub>)
+</p>
+where GÌ„<sub>K</sub> is the peak conductance of K<sup>+</sup> channel,
+n is the fraction of activation gates open. The transition from open
+to closed state has first order kinetics: <p> dn/dt = α<sub>n</sub> *
+( 1 - n) - β<sub>n</sub> * n </p>.
+
+The steady state values are:
+<p>
+n<sub>∞</sub> = α<sub>n</sub>/(α<sub>n</sub> + β<sub>n</sub>)
+</p>
+and time constant for steady state is:
+<p>
+τ<sub>n</sub> = 1/ (α<sub>n</sub> + β<sub>n</sub>)
+
+</p>
+and similarly for h.
+"""
+
+tooltip_Im = """<h3>Membrane current</h3>
+<p/>
+The current through the membrane is given by:
+<p>
+I<sub>m</sub> = C<sub>m</sub> dV/dt + I<sub>K</sub> + I<sub>Na</sub> + I<sub>L</sub>
+</p><p>
+ = C<sub>m</sub> dV/dt + G<sub>K</sub>(V, t) * (V - E<sub>K</sub>) + G<sub>Na</sub> * (V - E<sub>Na</sub>) + G<sub>L</sub> * (V - E<sub>L</sub>)
+</p>
+where G<sub>L</sub> is the leak current and E<sub>L</sub> is the leak reversal potential.
+
+"""
+
+default_line_edit_size = QtCore.QSize(80, 25)
+def set_default_line_edit_size(widget):
+ widget.setMinimumSize(default_line_edit_size)
+ widget.setMaximumSize(default_line_edit_size)
+
+class SquidGui( QMainWindow ):
+ defaults = {}
+ defaults.update(SquidAxon.defaults)
+ defaults.update(ClampCircuit.defaults)
+ defaults.update({'runtime': 50.0,
+ 'simdt': 0.01,
+ 'plotdt': 0.1,
+ 'vclamp.holdingV': 0.0,
+ 'vclamp.holdingT': 10.0,
+ 'vclamp.prepulseV': 0.0,
+ 'vclamp.prepulseT': 0.0,
+ 'vclamp.clampV': 50.0,
+ 'vclamp.clampT': 20.0,
+ 'iclamp.baseI': 0.0,
+ 'iclamp.firstI': 0.1,
+ 'iclamp.firstT': 40.0,
+ 'iclamp.firstD': 5.0,
+ 'iclamp.secondI': 0.0,
+ 'iclamp.secondT': 0.0,
+ 'iclamp.secondD': 0.0
+ })
+ def __init__(self, *args):
+ QMainWindow.__init__(self, *args)
+ self.squid_setup = SquidSetup()
+ self._plotdt = SquidGui.defaults['plotdt']
+ self._plot_dict = defaultdict(list)
+ self.setWindowTitle('Squid Axon simulation')
+ self.setDockNestingEnabled(True)
+ self._createRunControl()
+ self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._runControlDock)
+ self._runControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
+ self._createChannelControl()
+ self._channelCtrlBox.setWindowTitle('Channel properties')
+ self._channelControlDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
+ self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._channelControlDock)
+ self._createElectronicsControl()
+ self._electronicsDock.setFeatures(QDockWidget.AllDockWidgetFeatures)
+ self._electronicsDock.setWindowTitle('Electronics')
+ self.addDockWidget(QtCore.Qt.LeftDockWidgetArea, self._electronicsDock)
+ self._createPlotWidget()
+ self.setCentralWidget(self._plotWidget)
+ self._createStatePlotWidget()
+ self._createHelpMessage()
+ self._helpWindow.setVisible(False)
+ self._statePlotWidget.setWindowFlags(QtCore.Qt.Window)
+ self._statePlotWidget.setWindowTitle('State plot')
+ self._initActions()
+ self._createRunToolBar()
+ self._createPlotToolBar()
+
+ def getFloatInput(self, widget, name):
+ try:
+ return float(str(widget.text()))
+ except ValueError:
+ QMessageBox.critical(self, 'Invalid input', 'Please enter a valid number for {}'.format(name))
+ raise
+
+
+ def _createPlotWidget(self):
+ self._plotWidget = QWidget()
+ self._plotFigure = Figure()
+ self._plotCanvas = FigureCanvas(self._plotFigure)
+ self._plotCanvas.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+ self._plotCanvas.updateGeometry()
+ self._plotCanvas.setParent(self._plotWidget)
+ self._plotCanvas.mpl_connect('scroll_event', self._onScroll)
+ self._plotFigure.set_canvas(self._plotCanvas)
+ # Vm and command voltage go in the same subplot
+ self._vm_axes = self._plotFigure.add_subplot(2,2,1, title='Membrane potential')
+ self._vm_axes.set_ylim(-20.0, 120.0)
+ # Channel conductances go to the same subplot
+ self._g_axes = self._plotFigure.add_subplot(2,2,2, title='Channel conductance')
+ self._g_axes.set_ylim(0.0, 0.5)
+ # Injection current for Vclamp/Iclamp go to the same subplot
+ self._im_axes = self._plotFigure.add_subplot(2,2,3, title='Injection current')
+ self._im_axes.set_ylim(-0.5, 0.5)
+ # Channel currents go to the same subplot
+ self._i_axes = self._plotFigure.add_subplot(2,2,4, title='Channel current')
+ self._i_axes.set_ylim(-10, 10)
+ for axis in self._plotFigure.axes:
+ axis.set_autoscale_on(False)
+ layout = QVBoxLayout()
+ layout.addWidget(self._plotCanvas)
+ self._plotNavigator = NavigationToolbar(self._plotCanvas, self._plotWidget)
+ layout.addWidget(self._plotNavigator)
+ self._plotWidget.setLayout(layout)
+
+ def _createStatePlotWidget(self):
+ self._statePlotWidget = QWidget()
+ self._statePlotFigure = Figure()
+ self._statePlotCanvas = FigureCanvas(self._statePlotFigure)
+ self._statePlotCanvas.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+ self._statePlotCanvas.updateGeometry()
+ self._statePlotCanvas.setParent(self._statePlotWidget)
+ self._statePlotFigure.set_canvas(self._statePlotCanvas)
+ self._statePlotFigure.subplots_adjust(hspace=0.5)
+ self._statePlotAxes = self._statePlotFigure.add_subplot(2,1,1, title='State plot')
+ self._state_plot, = self._statePlotAxes.plot([], [], label='state')
+ self._activationParamAxes = self._statePlotFigure.add_subplot(2,1,2, title='H-H activation parameters vs time')
+ self._activationParamAxes.set_xlabel('Time (ms)')
+ #for axis in self._plotFigure.axes:
+ # axis.autoscale(False)
+ self._stateplot_xvar_label = QLabel('Variable on X-axis')
+ self._stateplot_xvar_combo = QComboBox()
+ self._stateplot_xvar_combo.addItems(['V', 'm', 'n', 'h'])
+ self._stateplot_xvar_combo.setCurrentIndex(0)
+ self._stateplot_xvar_combo.setEditable(False)
+ # self.connect(self._stateplot_xvar_combo,
+ # QtCore.SIGNAL('currentIndexChanged(const QString&)'),
+ # self._statePlotXSlot)
+ self._stateplot_xvar_combo.currentIndexChanged.connect( self._statePlotXSlot )
+ self._stateplot_yvar_label = QLabel('Variable on Y-axis')
+ self._stateplot_yvar_combo = QComboBox()
+ self._stateplot_yvar_combo.addItems(['V', 'm', 'n', 'h'])
+ self._stateplot_yvar_combo.setCurrentIndex(2)
+ self._stateplot_yvar_combo.setEditable(False)
+ self._stateplot_yvar_combo.currentIndexChanged.connect(self._statePlotYSlot)
+ self._statePlotNavigator = NavigationToolbar(self._statePlotCanvas, self._statePlotWidget)
+ frame = QFrame()
+ frame.setFrameStyle(QFrame.StyledPanel + QFrame.Raised)
+ layout = QHBoxLayout()
+ layout.addWidget(self._stateplot_xvar_label)
+ layout.addWidget(self._stateplot_xvar_combo)
+ layout.addWidget(self._stateplot_yvar_label)
+ layout.addWidget(self._stateplot_yvar_combo)
+ frame.setLayout(layout)
+ self._closeStatePlotAction = QAction('Close', self)
+ self._closeStatePlotAction.triggered.connect(self._statePlotWidget.close)
+ self._closeStatePlotButton = QToolButton()
+ self._closeStatePlotButton.setDefaultAction(self._closeStatePlotAction)
+ layout = QVBoxLayout()
+ layout.addWidget(frame)
+ layout.addWidget(self._statePlotCanvas)
+ layout.addWidget(self._statePlotNavigator)
+ layout.addWidget(self._closeStatePlotButton)
+ self._statePlotWidget.setLayout(layout)
+ # Setting the close event so that when the help window is
+ # closed the ``State plot`` button becomes unchecked
+ self._statePlotWidget.closeEvent = lambda event: self._showStatePlotAction.setChecked(False)
+
+ def _createRunControl(self):
+ self._runControlBox = QGroupBox(self)
+ self._runControlBox.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred)
+ self._runTimeLabel = QLabel("Run time (ms)", self._runControlBox)
+ self._simTimeStepLabel = QLabel("Simulation time step (ms)", self._runControlBox)
+ self._runTimeEdit = QLineEdit('%g' % (SquidGui.defaults['runtime']), self._runControlBox)
+ set_default_line_edit_size(self._runTimeEdit)
+ self._simTimeStepEdit = QLineEdit('%g' % (SquidGui.defaults['simdt']), self._runControlBox)
+ set_default_line_edit_size(self._simTimeStepEdit)
+ layout = QGridLayout()
+ layout.addWidget(self._runTimeLabel, 0, 0)
+ layout.addWidget(self._runTimeEdit, 0, 1)
+ layout.addWidget(self._simTimeStepLabel, 1, 0)
+ layout.addWidget(self._simTimeStepEdit, 1, 1)
+ layout.setColumnStretch(2, 1.0)
+ layout.setRowStretch(2, 1.0)
+ self._runControlBox.setLayout(layout)
+ self._runControlDock = QDockWidget('Simulation', self)
+ self._runControlDock.setWidget(self._runControlBox)
+
+ def _createChannelControl(self):
+ self._channelControlDock = QDockWidget('Channels', self)
+ self._channelCtrlBox = QGroupBox(self)
+ self._naConductanceToggle = QCheckBox('Block Na+ channel', self._channelCtrlBox)
+ self._naConductanceToggle.setToolTip('<html>%s</html>' % (tooltip_NaChan))
+ self._kConductanceToggle = QCheckBox('Block K+ channel', self._channelCtrlBox)
+ self._kConductanceToggle.setToolTip('<html>%s</html>' % (tooltip_KChan))
+ self._kOutLabel = QLabel('[K+]out (mM)', self._channelCtrlBox)
+ self._kOutEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.K_out),
+ self._channelCtrlBox)
+ self._kOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ self._kOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ set_default_line_edit_size(self._kOutEdit)
+ self._naOutLabel = QLabel('[Na+]out (mM)', self._channelCtrlBox)
+ self._naOutEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.Na_out),
+ self._channelCtrlBox)
+ self._naOutLabel.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ self._naOutEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ set_default_line_edit_size(self._naOutEdit)
+ self._kInLabel = QLabel('[K+]in (mM)', self._channelCtrlBox)
+ self._kInEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.K_in),
+ self._channelCtrlBox)
+ self._kInEdit.setToolTip(tooltip_Nernst)
+ self._naInLabel = QLabel('[Na+]in (mM)', self._channelCtrlBox)
+ self._naInEdit = QLineEdit('%g' % (self.squid_setup.squid_axon.Na_in),
+ self._channelCtrlBox)
+ self._naInEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ self._temperatureLabel = QLabel('Temperature (C)', self._channelCtrlBox)
+ self._temperatureEdit = QLineEdit('%g' % (self.defaults['temperature'] - CELSIUS_TO_KELVIN),
+ self._channelCtrlBox)
+ self._temperatureEdit.setToolTip('<html>%s</html>' % (tooltip_Nernst))
+ set_default_line_edit_size(self._temperatureEdit)
+ for child in self._channelCtrlBox.children():
+ if isinstance(child, QLineEdit):
+ set_default_line_edit_size(child)
+ layout = QGridLayout(self._channelCtrlBox)
+ layout.addWidget(self._naConductanceToggle, 0, 0)
+ layout.addWidget(self._kConductanceToggle, 1, 0)
+ layout.addWidget(self._naOutLabel, 2, 0)
+ layout.addWidget(self._naOutEdit, 2, 1)
+ layout.addWidget(self._naInLabel, 3, 0)
+ layout.addWidget(self._naInEdit, 3, 1)
+ layout.addWidget(self._kOutLabel, 4, 0)
+ layout.addWidget(self._kOutEdit, 4, 1)
+ layout.addWidget(self._kInLabel, 5, 0)
+ layout.addWidget(self._kInEdit, 5, 1)
+ layout.addWidget(self._temperatureLabel, 6, 0)
+ layout.addWidget(self._temperatureEdit, 6, 1)
+ layout.setRowStretch(7, 1.0)
+ self._channelCtrlBox.setLayout(layout)
+ self._channelControlDock.setWidget(self._channelCtrlBox)
+ return self._channelCtrlBox
+
+ def __get_stateplot_data(self, name):
+ data = []
+ if name == 'V':
+ data = self.squid_setup.vm_table.vector
+ elif name == 'm':
+ data = self.squid_setup.m_table.vector
+ elif name == 'h':
+ data = self.squid_setup.h_table.vector
+ elif name == 'n':
+ data = self.squid_setup.n_table.vector
+ else:
+ raise ValueError('Unrecognized selection: %s' % (name))
+ return numpy.asarray(data)
+
+ def _statePlotYSlot(self, selectedItem):
+ ydata = self.__get_stateplot_data(str(selectedItem))
+ self._state_plot.set_ydata(ydata)
+ self._statePlotAxes.set_ylabel(selectedItem)
+ if str(selectedItem) == 'V':
+ self._statePlotAxes.set_ylim(-20, 120)
+ else:
+ self._statePlotAxes.set_ylim(0, 1)
+ self._statePlotCanvas.draw()
+
+ def _statePlotXSlot(self, selectedItem):
+ xdata = self.__get_stateplot_data(str(selectedItem))
+ self._state_plot.set_xdata(xdata)
+ self._statePlotAxes.set_xlabel(selectedItem)
+ if str(selectedItem) == 'V':
+ self._statePlotAxes.set_xlim(-20, 120)
+ else:
+ self._statePlotAxes.set_xlim(0, 1)
+ self._statePlotCanvas.draw()
+
+ def _createElectronicsControl(self):
+ """Creates a tabbed widget of voltage clamp and current clamp controls"""
+ self._electronicsTab = QTabWidget(self)
+ self._electronicsTab.addTab(self._getIClampCtrlBox(), 'Current clamp')
+ self._electronicsTab.addTab(self._getVClampCtrlBox(), 'Voltage clamp')
+ self._electronicsDock = QDockWidget(self)
+ self._electronicsDock.setWidget(self._electronicsTab)
+
+ def _getVClampCtrlBox(self):
+ vClampPanel = QGroupBox(self)
+ self._vClampCtrlBox = vClampPanel
+ self._holdingVLabel = QLabel("Holding Voltage (mV)", vClampPanel)
+ self._holdingVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingV']), vClampPanel)
+ self._holdingTimeLabel = QLabel("Holding Time (ms)", vClampPanel)
+ self._holdingTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.holdingT']), vClampPanel)
+ self._prePulseVLabel = QLabel("Pre-pulse Voltage (mV)", vClampPanel)
+ self._prePulseVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseV']), vClampPanel)
+ self._prePulseTimeLabel = QLabel("Pre-pulse Time (ms)", vClampPanel)
+ self._prePulseTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.prepulseT']), vClampPanel)
+ self._clampVLabel = QLabel("Clamp Voltage (mV)", vClampPanel)
+ self._clampVEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.clampV']), vClampPanel)
+ self._clampTimeLabel = QLabel("Clamp Time (ms)", vClampPanel)
+ self._clampTimeEdit = QLineEdit('%g' % (SquidGui.defaults['vclamp.clampT']), vClampPanel)
+ for child in vClampPanel.children():
+ if isinstance(child, QLineEdit):
+ set_default_line_edit_size(child)
+ layout = QGridLayout(vClampPanel)
+ layout.addWidget(self._holdingVLabel, 0, 0)
+ layout.addWidget(self._holdingVEdit, 0, 1)
+ layout.addWidget(self._holdingTimeLabel, 1, 0)
+ layout.addWidget(self._holdingTimeEdit, 1, 1)
+ layout.addWidget(self._prePulseVLabel, 2, 0)
+ layout.addWidget(self._prePulseVEdit, 2, 1)
+ layout.addWidget(self._prePulseTimeLabel,3,0)
+ layout.addWidget(self._prePulseTimeEdit, 3, 1)
+ layout.addWidget(self._clampVLabel, 4, 0)
+ layout.addWidget(self._clampVEdit, 4, 1)
+ layout.addWidget(self._clampTimeLabel, 5, 0)
+ layout.addWidget(self._clampTimeEdit, 5, 1)
+ layout.setRowStretch(6, 1.0)
+ vClampPanel.setLayout(layout)
+ return self._vClampCtrlBox
+
+ def _getIClampCtrlBox(self):
+ iClampPanel = QGroupBox(self)
+ self._iClampCtrlBox = iClampPanel
+ self._baseCurrentLabel = QLabel("Base Current Level (uA)",iClampPanel)
+ self._baseCurrentEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.baseI']),iClampPanel)
+ self._firstPulseLabel = QLabel("First Pulse Current (uA)", iClampPanel)
+ self._firstPulseEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstI']), iClampPanel)
+ self._firstDelayLabel = QLabel("First Onset Delay (ms)", iClampPanel)
+ self._firstDelayEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstD']),iClampPanel)
+ self._firstPulseWidthLabel = QLabel("First Pulse Width (ms)", iClampPanel)
+ self._firstPulseWidthEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.firstT']), iClampPanel)
+ self._secondPulseLabel = QLabel("Second Pulse Current (uA)", iClampPanel)
+ self._secondPulseEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondI']), iClampPanel)
+ self._secondDelayLabel = QLabel("Second Onset Delay (ms)", iClampPanel)
+ self._secondDelayEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondD']),iClampPanel)
+ self._secondPulseWidthLabel = QLabel("Second Pulse Width (ms)", iClampPanel)
+ self._secondPulseWidthEdit = QLineEdit('%g' % (SquidGui.defaults['iclamp.secondT']), iClampPanel)
+ self._pulseMode = QComboBox(iClampPanel)
+ self._pulseMode.addItem("Single Pulse")
+ self._pulseMode.addItem("Pulse Train")
+ for child in iClampPanel.children():
+ if isinstance(child, QLineEdit):
+ set_default_line_edit_size(child)
+ layout = QGridLayout(iClampPanel)
+ layout.addWidget(self._baseCurrentLabel, 0, 0)
+ layout.addWidget(self._baseCurrentEdit, 0, 1)
+ layout.addWidget(self._firstPulseLabel, 1, 0)
+ layout.addWidget(self._firstPulseEdit, 1, 1)
+ layout.addWidget(self._firstDelayLabel, 2, 0)
+ layout.addWidget(self._firstDelayEdit, 2, 1)
+ layout.addWidget(self._firstPulseWidthLabel, 3, 0)
+ layout.addWidget(self._firstPulseWidthEdit, 3, 1)
+ layout.addWidget(self._secondPulseLabel, 4, 0)
+ layout.addWidget(self._secondPulseEdit, 4, 1)
+ layout.addWidget(self._secondDelayLabel, 5, 0)
+ layout.addWidget(self._secondDelayEdit, 5, 1)
+ layout.addWidget(self._secondPulseWidthLabel, 6, 0)
+ layout.addWidget(self._secondPulseWidthEdit, 6, 1)
+ layout.addWidget(self._pulseMode, 7, 0, 1, 2)
+ layout.setRowStretch(8, 1.0)
+ # layout.setSizeConstraint(QLayout.SetFixedSize)
+ iClampPanel.setLayout(layout)
+ return self._iClampCtrlBox
+
+ def _overlayPlots(self, overlay):
+ if not overlay:
+ for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
+ title = axis.get_title()
+ axis.clear()
+ axis.set_title(title)
+ suffix = ''
+ else:
+ suffix = '_%d' % (len(self._plot_dict['vm']))
+ self._vm_axes.set_xlim(0.0, self._runtime)
+ self._g_axes.set_xlim(0.0, self._runtime)
+ self._im_axes.set_xlim(0.0, self._runtime)
+ self._i_axes.set_xlim(0.0, self._runtime)
+ self._vm_plot, = self._vm_axes.plot([], [], label='Vm%s'%(suffix))
+ self._plot_dict['vm'].append(self._vm_plot)
+ self._command_plot, = self._vm_axes.plot([], [], label='command%s'%(suffix))
+ self._plot_dict['command'].append(self._command_plot)
+ # Channel conductances go to the same subplot
+ self._gna_plot, = self._g_axes.plot([], [], label='Na%s'%(suffix))
+ self._plot_dict['gna'].append(self._gna_plot)
+ self._gk_plot, = self._g_axes.plot([], [], label='K%s'%(suffix))
+ self._plot_dict['gk'].append(self._gk_plot)
+ # Injection current for Vclamp/Iclamp go to the same subplot
+ self._iclamp_plot, = self._im_axes.plot([], [], label='Iclamp%s'%(suffix))
+ self._vclamp_plot, = self._im_axes.plot([], [], label='Vclamp%s'%(suffix))
+ self._plot_dict['iclamp'].append(self._iclamp_plot)
+ self._plot_dict['vclamp'].append(self._vclamp_plot)
+ # Channel currents go to the same subplot
+ self._ina_plot, = self._i_axes.plot([], [], label='Na%s'%(suffix))
+ self._plot_dict['ina'].append(self._ina_plot)
+ self._ik_plot, = self._i_axes.plot([], [], label='K%s'%(suffix))
+ self._plot_dict['ik'].append(self._ik_plot)
+ # self._i_axes.legend()
+ # State plots
+ self._state_plot, = self._statePlotAxes.plot([], [], label='state%s'%(suffix))
+ self._plot_dict['state'].append(self._state_plot)
+ self._m_plot, = self._activationParamAxes.plot([],[], label='m%s'%(suffix))
+ self._h_plot, = self._activationParamAxes.plot([], [], label='h%s'%(suffix))
+ self._n_plot, = self._activationParamAxes.plot([], [], label='n%s'%(suffix))
+ self._plot_dict['m'].append(self._m_plot)
+ self._plot_dict['h'].append(self._h_plot)
+ self._plot_dict['n'].append(self._n_plot)
+ if self._showLegendAction.isChecked():
+ for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
+ axis.legend()
+
+ def _updateAllPlots(self):
+ self._updatePlots()
+ self._updateStatePlot()
+
+ def _updatePlots(self):
+ if len(self.squid_setup.vm_table.vector) <= 0:
+ return
+ vm = numpy.asarray(self.squid_setup.vm_table.vector)
+ cmd = numpy.asarray(self.squid_setup.cmd_table.vector)
+ ik = numpy.asarray(self.squid_setup.ik_table.vector)
+ ina = numpy.asarray(self.squid_setup.ina_table.vector)
+ iclamp = numpy.asarray(self.squid_setup.iclamp_table.vector)
+ vclamp = numpy.asarray(self.squid_setup.vclamp_table.vector)
+ gk = numpy.asarray(self.squid_setup.gk_table.vector)
+ gna = numpy.asarray(self.squid_setup.gna_table.vector)
+ time_series = numpy.linspace(0, self._plotdt * len(vm), len(vm))
+ self._vm_plot.set_data(time_series, vm)
+ time_series = numpy.linspace(0, self._plotdt * len(cmd), len(cmd))
+ self._command_plot.set_data(time_series, cmd)
+ time_series = numpy.linspace(0, self._plotdt * len(ik), len(ik))
+ self._ik_plot.set_data(time_series, ik)
+ time_series = numpy.linspace(0, self._plotdt * len(ina), len(ina))
+ self._ina_plot.set_data(time_series, ina)
+ time_series = numpy.linspace(0, self._plotdt * len(iclamp), len(iclamp))
+ self._iclamp_plot.set_data(time_series, iclamp)
+ time_series = numpy.linspace(0, self._plotdt * len(vclamp), len(vclamp))
+ self._vclamp_plot.set_data(time_series, vclamp)
+ time_series = numpy.linspace(0, self._plotdt * len(gk), len(gk))
+ self._gk_plot.set_data(time_series, gk)
+ time_series = numpy.linspace(0, self._plotdt * len(gna), len(gna))
+ self._gna_plot.set_data(time_series, gna)
+ # self._vm_axes.margins(y=0.1)
+ # self._g_axes.margin(y=0.1)
+ # self._im_axes.margins(y=0.1)
+ # self._i_axes.margins(y=0.1)
+ if self._autoscaleAction.isChecked():
+ for axis in self._plotFigure.axes:
+ axis.relim()
+ axis.margins(0.1, 0.1)
+ axis.autoscale_view(tight=True)
+ else:
+ self._vm_axes.set_ylim(-20.0, 120.0)
+ self._g_axes.set_ylim(0.0, 0.5)
+ self._im_axes.set_ylim(-0.5, 0.5)
+ self._i_axes.set_ylim(-10, 10)
+ self._vm_axes.set_xlim(0.0, time_series[-1])
+ self._g_axes.set_xlim(0.0, time_series[-1])
+ self._im_axes.set_xlim(0.0, time_series[-1])
+ self._i_axes.set_xlim(0.0, time_series[-1])
+ self._plotCanvas.draw()
+
+ def _updateStatePlot(self):
+ if len(self.squid_setup.vm_table.vector) <= 0:
+ return
+ sx = str(self._stateplot_xvar_combo.currentText())
+ sy = str(self._stateplot_yvar_combo.currentText())
+ xdata = self.__get_stateplot_data(sx)
+ ydata = self.__get_stateplot_data(sy)
+ minlen = min(len(xdata), len(ydata))
+ self._state_plot.set_data(xdata[:minlen], ydata[:minlen])
+ self._statePlotAxes.set_xlabel(sx)
+ self._statePlotAxes.set_ylabel(sy)
+ if sx == 'V':
+ self._statePlotAxes.set_xlim(-20, 120)
+ else:
+ self._statePlotAxes.set_xlim(0, 1)
+ if sy == 'V':
+ self._statePlotAxes.set_ylim(-20, 120)
+ else:
+ self._statePlotAxes.set_ylim(0, 1)
+ self._activationParamAxes.set_xlim(0, self._runtime)
+ m = self.__get_stateplot_data('m')
+ n = self.__get_stateplot_data('n')
+ h = self.__get_stateplot_data('h')
+ time_series = numpy.linspace(0, self._plotdt*len(m), len(m))
+ self._m_plot.set_data(time_series, m)
+ time_series = numpy.linspace(0, self._plotdt*len(h), len(h))
+ self._h_plot.set_data(time_series, h)
+ time_series = numpy.linspace(0, self._plotdt*len(n), len(n))
+ self._n_plot.set_data(time_series, n)
+ if self._autoscaleAction.isChecked():
+ for axis in self._statePlotFigure.axes:
+ axis.relim()
+ axis.set_autoscale_on(True)
+ axis.autoscale_view(True)
+ self._statePlotCanvas.draw()
+
+ def _runSlot(self):
+ if moose.isRunning():
+ print('Stopping simulation in progress ...')
+ moose.stop()
+ self._runtime = self.getFloatInput(self._runTimeEdit, self._runTimeLabel.text())
+ self._overlayPlots(self._overlayAction.isChecked())
+ self._simdt = self.getFloatInput(self._simTimeStepEdit, self._simTimeStepLabel.text())
+ clampMode = None
+ singlePulse = True
+ if self._electronicsTab.currentWidget() == self._vClampCtrlBox:
+ clampMode = 'vclamp'
+ baseLevel = self.getFloatInput(self._holdingVEdit, self._holdingVLabel.text())
+ firstDelay = self.getFloatInput(self._holdingTimeEdit, self._holdingTimeLabel.text())
+ firstWidth = self.getFloatInput(self._prePulseTimeEdit, self._prePulseTimeLabel.text())
+ firstLevel = self.getFloatInput(self._prePulseVEdit, self._prePulseVLabel.text())
+ secondDelay = firstWidth
+ secondWidth = self.getFloatInput(self._clampTimeEdit, self._clampTimeLabel.text())
+ secondLevel = self.getFloatInput(self._clampVEdit, self._clampVLabel.text())
+ if not self._autoscaleAction.isChecked():
+ self._im_axes.set_ylim(-10.0, 10.0)
+ else:
+ clampMode = 'iclamp'
+ baseLevel = self.getFloatInput(self._baseCurrentEdit, self._baseCurrentLabel.text())
+ firstDelay = self.getFloatInput(self._firstDelayEdit, self._firstDelayLabel.text())
+ firstWidth = self.getFloatInput(self._firstPulseWidthEdit, self._firstPulseWidthLabel.text())
+ firstLevel = self.getFloatInput(self._firstPulseEdit, self._firstPulseLabel.text())
+ secondDelay = self.getFloatInput(self._secondDelayEdit, self._secondDelayLabel.text())
+ secondLevel = self.getFloatInput(self._secondPulseEdit, self._secondPulseLabel.text())
+ secondWidth = self.getFloatInput(self._secondPulseWidthEdit, self._secondPulseWidthLabel.text())
+ singlePulse = (self._pulseMode.currentIndex() == 0)
+ if not self._autoscaleAction.isChecked():
+ self._im_axes.set_ylim(-0.4, 0.4)
+ self.squid_setup.clamp_ckt.configure_pulses(baseLevel=baseLevel,
+ firstDelay=firstDelay,
+ firstWidth=firstWidth,
+ firstLevel=firstLevel,
+ secondDelay=secondDelay,
+ secondWidth=secondWidth,
+ secondLevel=secondLevel,
+ singlePulse=singlePulse)
+ if self._kConductanceToggle.isChecked():
+ self.squid_setup.squid_axon.specific_gK = 0.0
+ else:
+ self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults['specific_gK']
+ if self._naConductanceToggle.isChecked():
+ self.squid_setup.squid_axon.specific_gNa = 0.0
+ else:
+ self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults['specific_gNa']
+ self.squid_setup.squid_axon.celsius = self.getFloatInput(self._temperatureEdit, self._temperatureLabel.text())
+ self.squid_setup.squid_axon.K_out = self.getFloatInput(self._kOutEdit, self._kOutLabel.text())
+ self.squid_setup.squid_axon.Na_out = self.getFloatInput(self._naOutEdit, self._naOutLabel.text())
+ self.squid_setup.squid_axon.K_in = self.getFloatInput(self._kInEdit, self._kInLabel.text())
+ self.squid_setup.squid_axon.Na_in = self.getFloatInput(self._naInEdit, self._naInLabel.text())
+ self.squid_setup.squid_axon.updateEk()
+ self.squid_setup.schedule(self._simdt, self._plotdt, clampMode)
+ # The following line is for use with Qthread
+ self.squid_setup.run(self._runtime)
+ self._updateAllPlots()
+
+ def _toggleDocking(self, on):
+ self._channelControlDock.setFloating(on)
+ self._electronicsDock.setFloating(on)
+ self._runControlDock.setFloating(on)
+
+ def _restoreDocks(self):
+ self._channelControlDock.setVisible(True)
+ self._electronicsDock.setVisible(True)
+ self._runControlDock.setVisible(True)
+
+ def _initActions(self):
+ self._runAction = QAction(self.tr('Run'), self)
+ self._runAction.setShortcut(self.tr('F5'))
+ self._runAction.setToolTip('Run simulation (F5)')
+ self._runAction.triggered.connect( self._runSlot)
+ self._resetToDefaultsAction = QAction(self.tr('Restore defaults'), self)
+ self._resetToDefaultsAction.setToolTip('Reset all settings to their default values')
+ self._resetToDefaultsAction.triggered.connect( self._useDefaults)
+ self._showLegendAction = QAction(self.tr('Display legend'), self)
+ self._showLegendAction.setCheckable(True)
+ self._showLegendAction.toggled.connect(self._showLegend)
+ self._showStatePlotAction = QAction(self.tr('State plot'), self)
+ self._showStatePlotAction.setCheckable(True)
+ self._showStatePlotAction.setChecked(False)
+ self._showStatePlotAction.toggled.connect(self._statePlotWidget.setVisible)
+ self._autoscaleAction = QAction(self.tr('Auto-scale plots'), self)
+ self._autoscaleAction.setCheckable(True)
+ self._autoscaleAction.setChecked(False)
+ self._autoscaleAction.toggled.connect(self._autoscale)
+ self._overlayAction = QAction('Overlay plots', self)
+ self._overlayAction.setCheckable(True)
+ self._overlayAction.setChecked(False)
+ self._dockAction = QAction('Undock all', self)
+ self._dockAction.setCheckable(True)
+ self._dockAction.setChecked(False)
+ # self._dockAction.toggle.connect( self._toggleDocking)
+ self._restoreDocksAction = QAction('Show all', self)
+ self._restoreDocksAction.triggered.connect( self._restoreDocks)
+ self._quitAction = QAction(self.tr('&Quit'), self)
+ self._quitAction.setShortcut(self.tr('Ctrl+Q'))
+ self._quitAction.triggered.connect(qApp.closeAllWindows)
+
+
+
+ def _createRunToolBar(self):
+ self._simToolBar = self.addToolBar(self.tr('Simulation control'))
+ self._simToolBar.addAction(self._quitAction)
+ self._simToolBar.addAction(self._runAction)
+ self._simToolBar.addAction(self._resetToDefaultsAction)
+ self._simToolBar.addAction(self._dockAction)
+ self._simToolBar.addAction(self._restoreDocksAction)
+
+ def _createPlotToolBar(self):
+ self._plotToolBar = self.addToolBar(self.tr('Plotting control'))
+ self._plotToolBar.addAction(self._showLegendAction)
+ self._plotToolBar.addAction(self._autoscaleAction)
+ self._plotToolBar.addAction(self._overlayAction)
+ self._plotToolBar.addAction(self._showStatePlotAction)
+ self._plotToolBar.addAction(self._helpAction)
+ self._plotToolBar.addAction(self._helpBiophysicsAction)
+
+ def _showLegend(self, on):
+ if on:
+ for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
+ axis.legend().set_visible(True)
+ else:
+ for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
+ axis.legend().set_visible(False)
+ self._plotCanvas.draw()
+ self._statePlotCanvas.draw()
+
+ def _autoscale(self, on):
+ if on:
+ for axis in (self._plotFigure.axes + self._statePlotFigure.axes):
+ axis.relim()
+ axis.set_autoscale_on(True)
+ axis.autoscale_view(True)
+ else:
+ for axis in self._plotFigure.axes:
+ axis.set_autoscale_on(False)
+ self._vm_axes.set_ylim(-20.0, 120.0)
+ self._g_axes.set_ylim(0.0, 0.5)
+ self._im_axes.set_ylim(-0.5, 0.5)
+ self._i_axes.set_ylim(-10, 10)
+ self._plotCanvas.draw()
+ self._statePlotCanvas.draw()
+
+ def _useDefaults(self):
+ self._runTimeEdit.setText('%g' % (self.defaults['runtime']))
+ self._simTimeStepEdit.setText('%g' % (self.defaults['simdt']))
+ self._overlayAction.setChecked(False)
+ self._naConductanceToggle.setChecked(False)
+ self._kConductanceToggle.setChecked(False)
+ self._kOutEdit.setText('%g' % (SquidGui.defaults['K_out']))
+ self._naOutEdit.setText('%g' % (SquidGui.defaults['Na_out']))
+ self._kInEdit.setText('%g' % (SquidGui.defaults['K_in']))
+ self._naInEdit.setText('%g' % (SquidGui.defaults['Na_in']))
+ self._temperatureEdit.setText('%g' % (SquidGui.defaults['temperature'] - CELSIUS_TO_KELVIN))
+ self._holdingVEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingV']))
+ self._holdingTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.holdingT']))
+ self._prePulseVEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseV']))
+ self._prePulseTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.prepulseT']))
+ self._clampVEdit.setText('%g' % (SquidGui.defaults['vclamp.clampV']))
+ self._clampTimeEdit.setText('%g' % (SquidGui.defaults['vclamp.clampT']))
+ self._baseCurrentEdit.setText('%g' % (SquidGui.defaults['iclamp.baseI']))
+ self._firstPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.firstI']))
+ self._firstDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.firstD']))
+ self._firstPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.firstT']))
+ self._secondPulseEdit.setText('%g' % (SquidGui.defaults['iclamp.secondI']))
+ self._secondDelayEdit.setText('%g' % (SquidGui.defaults['iclamp.secondD']))
+ self._secondPulseWidthEdit.setText('%g' % (SquidGui.defaults['iclamp.secondT']))
+ self._pulseMode.setCurrentIndex(0)
+
+ def _onScroll(self, event):
+ if event.inaxes is None:
+ return
+ axes = event.inaxes
+ zoom = 0.0
+ if event.button == 'up':
+ zoom = -1.0
+ elif event.button == 'down':
+ zoom = 1.0
+ if zoom != 0.0:
+ self._plotNavigator.push_current()
+ axes.get_xaxis().zoom(zoom)
+ axes.get_yaxis().zoom(zoom)
+ self._plotCanvas.draw()
+
+ def closeEvent(self, event):
+ qApp.closeAllWindows()
+
+ def _showBioPhysicsHelp(self):
+ self._createHelpMessage()
+ self._helpMessageText.setText('<html><p>%s</p><p>%s</p><p>%s</p><p>%s</p><p>%s</p></html>' %
+ (tooltip_Nernst,
+ tooltip_Erest,
+ tooltip_KChan,
+ tooltip_NaChan,
+ tooltip_Im))
+ self._helpWindow.setVisible(True)
+
+ def _showRunningHelp(self):
+ self._createHelpMessage()
+ self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
+ self._helpWindow.setVisible(True)
+
+ def _createHelpMessage(self):
+ if hasattr(self, '_helpWindow'):
+ return
+ self._helpWindow = QWidget()
+ self._helpWindow.setWindowFlags(QtCore.Qt.Window)
+ layout = QVBoxLayout()
+ self._helpWindow.setLayout(layout)
+ self._helpMessageArea = QScrollArea()
+ self._helpMessageText = QTextBrowser()
+ self._helpMessageText.setOpenExternalLinks(True)
+ self._helpMessageArea.setWidget(self._helpMessageText)
+ layout.addWidget(self._helpMessageText)
+ self._squidGuiPath = os.path.dirname(os.path.abspath(__file__))
+ self._helpBaseURL = os.path.join(self._squidGuiPath,'help.html')
+ self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
+ self._helpMessageText.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+ self._helpMessageArea.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
+ self._helpMessageText.setMinimumSize(800, 600)
+ self._closeHelpAction = QAction('Close', self)
+ self._closeHelpAction.triggered.connect(self._helpWindow.close)
+ # Setting the close event so that the ``Help`` button is
+ # unchecked when the help window is closed
+ self._helpWindow.closeEvent = lambda event: self._helpAction.setChecked(False)
+ self._helpTOCAction = QAction('Help running demo', self)
+ self._helpTOCAction.triggered.connect( self._jumpToHelpTOC)
+ # This panel is for putting two buttons using horizontal
+ # layout
+ panel = QFrame()
+ panel.setFrameStyle(QFrame.StyledPanel + QFrame.Raised)
+ layout.addWidget(panel)
+ layout = QHBoxLayout()
+ panel.setLayout(layout)
+ self._helpAction = QAction('Help running', self)
+ self._helpAction.triggered.connect(self._showRunningHelp)
+ self._helpBiophysicsAction = QAction('Help biophysics', self)
+ self._helpBiophysicsAction.triggered.connect(self._showBioPhysicsHelp)
+ self._helpTOCButton = QToolButton()
+ self._helpTOCButton.setDefaultAction(self._helpTOCAction)
+ self._helpBiophysicsButton = QToolButton()
+ self._helpBiophysicsButton.setDefaultAction(self._helpBiophysicsAction)
+ layout.addWidget(self._helpTOCButton)
+ layout.addWidget(self._helpBiophysicsButton)
+ self._closeHelpButton = QToolButton()
+ self._closeHelpButton.setDefaultAction(self._closeHelpAction)
+ layout.addWidget(self._closeHelpButton)
+
+ def _jumpToHelpTOC(self):
+ self._helpMessageText.setSource(QtCore.QUrl(self._helpBaseURL))
+
+if __name__ == '__main__':
+ app = QApplication(sys.argv)
+ # app.connect(app, QtCore.SIGNAL('lastWindowClosed()'), app, QtCore.SLOT('quit()'))
+ app.quitOnLastWindowClosed( )
+ qApp = app
+ squid_gui = SquidGui()
+ squid_gui.show()
+ print(squid_gui.size())
+ sys.exit(app.exec_())
+
+#
+# squidgui.py ends here
diff --git a/moose-examples/squid/test_squid.py b/moose-examples/squid/test_squid.py
index 005cb162..5bbef8bc 100644
--- a/moose-examples/squid/test_squid.py
+++ b/moose-examples/squid/test_squid.py
@@ -30,6 +30,7 @@
import unittest
import pylab
+import numpy
from squid import SquidModel
class SquidAxonTest(unittest.TestCase):
@@ -112,6 +113,5 @@ class SquidAxonTest(unittest.TestCase):
self.assertLessEqual(difference, numpy.mean(beta_m)*1e-6)
-
#
# test_squid.py ends here
diff --git a/moose-examples/tutorials/Electrophys/CableInjectEquivCkt.png b/moose-examples/tutorials/Electrophys/CableInjectEquivCkt.png
new file mode 100644
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diff --git a/moose-examples/tutorials/Electrophys/README.txt b/moose-examples/tutorials/Electrophys/README.txt
new file mode 100644
index 00000000..585fd34e
--- /dev/null
+++ b/moose-examples/tutorials/Electrophys/README.txt
@@ -0,0 +1,80 @@
+This is a list of files in the Electrophys tutorials directory
+
+ephys1_cable.py:
+
+This is a model of a simple uniform passive cable. It has two plots: one
+of membrane potential Vm as a function of time, sampled at four locations
+along the cable, and the other of Vm as a function of position, sampled at
+5 times (intervals of 5 ms) during the simulation.
+The user can use the sliders to scale the following parameters up and down:
+RM
+RA
+CM
+length
+diameter
+
+In addition, the user can toggle between a long (steady-state) current
+injection stimulus, and a brief pulse of 1 ms.
+
+Finally, when the user hits "Quit" the time-series of the soma compartment
+is printed out.
+
+Things to do:
+1. Vary diameter, length, RM, CM, RA. Check that the decay behaves as per
+ cable theory. Get an intuition for these.
+2. Check that lambda (length constant) is according to equations. Check
+ how much decay there is for different L (electrotonic length).
+2a. Note that if the cable is shorter than L, the signal doesn't decay so
+ well. Why?
+2b. Convince yourself that you'll never see a passive signal along a long
+ axon.
+3. Examine propagation of the depolarization for a brief current pulse.
+ Look for the three signatures of propagation along a dendrite.
+4. Run a simulation of the long stimulus. When you hit Quit, the program will
+ dump the soma potential charging time-course into a file. Check that
+ the tau (time-constant) of the soma is according to equations when the
+ L is very small, but deviates when it is longer. Use Rall's expression
+ for L as a function of the time-courses of soma depolarization.
+
+
+
+ephys2_Rall_law.py:
+
+This explores the implication of Rall's Law and cable branching.
+This is a model of a branched cell, compared with the model of a uniform
+cylindrical cell. The sliders vary the parameters of the branches. Two
+time-points are displayed; 10 ms and 50 ms.
+
+Things to do:
+1. Vary all the passive parameters of branches, see how they affect the
+ propagation past the branch point.
+2. Match up the branched cell (blue plot/dots) to the cylinder (red line).
+ See if the resultant parameters obey Rall's Law.
+
+Todo: - Stimuli in any end or both dend ends.
+
+Neuronal summation
+ - Synaptic input at Y tips and branch point, both I and E.
+ - Vary weights
+ - Vary time since start for each.
+ - Vary taus of I.
+ - Have spiking soma, to set up thresholding as an option.
+
+Channel mixer:
+ - Modulate the conductance of battery of channels
+ - Modulate Ca_conc tau
+ - Plot Ca and Vm
+ - Set different stim pulse amplitude and duration.
+
+NMDA receptor and associativity:
+ - Plot Vm and Ca
+ - Give glu and NMDA input different time and different ampl
+
+AP propagation:
+ - Vary dia
+ - Vary RM, CM, RA
+ - Vary channel densities
+
+Squid demo:
+ - Already have it.
+
diff --git a/moose-examples/tutorials/Electrophys/RallsLaw.png b/moose-examples/tutorials/Electrophys/RallsLaw.png
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diff --git a/moose-examples/tutorials/Electrophys/ephys1_cable.py b/moose-examples/tutorials/Electrophys/ephys1_cable.py
new file mode 100644
index 00000000..515ea4fd
--- /dev/null
+++ b/moose-examples/tutorials/Electrophys/ephys1_cable.py
@@ -0,0 +1,212 @@
+########################################################################
+# This example demonstrates a cable
+# Copyright (C) Upinder S. Bhalla NCBS 2018
+# Released under the terms of the GNU Public License V3.
+########################################################################
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+from matplotlib.widgets import Slider, Button
+import numpy as np
+import warnings
+import moose
+import rdesigneur as rd
+
+numDendSeg = 50
+interval = 0.005
+lines = []
+tplot = []
+RM = 1.0
+RA = 1.0
+CM = 0.01
+length = 0.002
+dia = 1e-6
+stimStr = "2e-10"
+runtime = 50e-3
+elecPlotDt = 0.001
+
+def makeModel():
+ segLen = length / numDendSeg
+ rdes = rd.rdesigneur(
+ stealCellFromLibrary = True,
+ elecPlotDt = elecPlotDt,
+ verbose = False,
+ # cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
+ # The numerical arguments are all optional
+ cellProto =
+ [['ballAndStick', 'soma', dia, segLen, dia, length, numDendSeg]],
+ passiveDistrib = [[ '#', 'RM', str(RM), 'CM', str(CM), 'RA', str(RA) ]],
+ stimList = [['soma', '1', '.', 'inject', stimStr ]],
+ plotList = [['dend3,dend18,dend33,dend49', '1', '.', 'Vm' ]],
+ )
+ rdes.buildModel()
+
+def main():
+ global vec
+ warnings.filterwarnings("ignore", category=UserWarning, module="matplotlib")
+ makeDisplay()
+ quit()
+
+def updateRM(RM_):
+ global RM
+ RM = RM_
+ updateDisplay()
+
+def updateCM(CM_):
+ global CM
+ CM = CM_
+ updateDisplay()
+
+def updateRA(RA_):
+ global RA
+ RA = RA_
+ updateDisplay()
+
+def updateLen(val): # This does the length of the entire cell.
+ global length
+ length = val * 0.001
+ updateDisplay()
+
+def updateDia(val):
+ global dia
+ dia = val * 1e-6
+ updateDisplay()
+
+class stimToggle():
+ def __init__( self, toggle, ax ):
+ self.duration = 1
+ self.toggle = toggle
+ self.ax = ax
+
+ def click( self, event ):
+ global stimStr
+ if self.duration < 0.5:
+ self.duration = 1.0
+ self.toggle.label.set_text( "Long Stim" )
+ self.toggle.color = "yellow"
+ self.toggle.hovercolor = "yellow"
+ stimStr = "2e-10"
+ else:
+ self.duration = 0.001
+ self.toggle.label.set_text( "Short Stim" )
+ self.toggle.color = "orange"
+ self.toggle.hovercolor = "orange"
+ stimStr = "1e-9*(t<0.001)"
+ #stimStr = "10e-9*(t<0.001)-9e-9*(t>0.001&&t<0.002)"
+ updateDisplay()
+
+def updateDisplay():
+ makeModel()
+ vec = moose.wildcardFind( '/model/elec/#[ISA=CompartmentBase]' )
+ tabvec = moose.wildcardFind( '/model/graphs/plot#' )
+ #vec[0].inject = 1e-10
+ moose.reinit()
+ initdt = 0.0001
+ dt = initdt
+ currtime = 0.0
+ for i in lines:
+ moose.start( dt )
+ currtime += dt
+ i.set_ydata( [v.Vm * 1000 for v in vec] )
+ dt = interval
+ #print( "inRunSim v0={}, v10={}".format( vec[0].Vm, vec[10].Vm ) )
+ moose.start( runtime - currtime )
+ for i,tab in zip( tplot, tabvec ):
+ i.set_ydata( tab.vector * 1000 )
+
+ moose.delete( '/model' )
+ moose.delete( '/library' )
+ # Put in something here for the time-series on soma
+
+def doQuit( event ):
+ tab = []
+ makeModel()
+ soma = moose.element( '/model/elec/soma' )
+ moose.reinit()
+ with open('output.txt', 'w') as file:
+ file.write( "0.000 {:.2f}\n".format( soma.Vm * 1000 ) )
+ for t in np.arange( 0, 0.1, 0.001 ):
+ moose.start(0.001)
+ file.write( "{:.3f} {:.2f}\n".format( t+0.001, soma.Vm*1000 ) )
+ quit()
+
+def makeDisplay():
+ global tplot
+ global lines
+ #img = mpimg.imread( 'CableEquivCkt.png' )
+ img = mpimg.imread( 'CableInjectEquivCkt.png' )
+ #plt.ion()
+ fig = plt.figure( figsize=(10,12) )
+ png = fig.add_subplot(321)
+ imgplot = plt.imshow( img )
+ plt.axis('off')
+ ax1 = fig.add_subplot(322)
+ plt.ylabel( 'Vm (mV)' )
+ plt.ylim( -80, 40 )
+ plt.xlabel( 'time (ms)' )
+ plt.title( "Membrane potential vs time at 4 positions." )
+ t = np.arange( 0.0, runtime + elecPlotDt / 2.0, elecPlotDt ) * 1000 #ms
+ for i,col,name in zip( range( 4 ), ['b-', 'g-', 'r-', 'm-' ], ['a', 'b', 'c', 'd'] ):
+ ln, = ax1.plot( t, np.zeros(len(t)), col, label='pos= ' + name )
+ tplot.append(ln)
+ plt.legend()
+
+ ax2 = fig.add_subplot(312)
+ #ax2.margins( 0.05 )
+ #ax.set_ylim( 0, 0.1 )
+ plt.ylabel( 'Vm (mV)' )
+ plt.ylim( -80, 50 )
+ plt.xlabel( 'Position (microns)' )
+ #ax2.autoscale( enable = True, axis = 'y' )
+ plt.title( "Membrane potential vs position, at 5 times." )
+ t = np.arange( 0, numDendSeg+1, 1 ) #sec
+ for i,col in zip( range( 5 ), ['k-', 'b-', 'g-', 'y-', 'm-' ] ):
+ ln, = ax2.plot( t, np.zeros(numDendSeg+1), col, label="t={}".format(i*interval) )
+ lines.append(ln)
+ plt.legend()
+ ax = fig.add_subplot(313)
+ #ax.margins( 0.05 )
+ plt.axis('off')
+ axcolor = 'palegreen'
+ axStim = plt.axes( [0.02,0.05, 0.20,0.03], facecolor='green' )
+ axReset = plt.axes( [0.25,0.05, 0.30,0.03], facecolor='blue' )
+ axQuit = plt.axes( [0.60,0.05, 0.30,0.03], facecolor='blue' )
+ axRM = plt.axes( [0.25,0.1, 0.65,0.03], facecolor=axcolor )
+ axCM = plt.axes( [0.25,0.15, 0.65,0.03], facecolor=axcolor )
+ axRA = plt.axes( [0.25,0.20, 0.65,0.03], facecolor=axcolor )
+ axLen = plt.axes( [0.25,0.25, 0.65,0.03], facecolor=axcolor )
+ axDia = plt.axes( [0.25,0.30, 0.65,0.03], facecolor=axcolor )
+ #aInit = Slider( axAinit, 'A init conc', 0, 10, valinit=1.0, valstep=0.2)
+ stim = Button( axStim, 'Long Stim', color = 'yellow' )
+ stimObj = stimToggle( stim, axStim )
+
+ reset = Button( axReset, 'Reset', color = 'cyan' )
+ q = Button( axQuit, 'Quit', color = 'pink' )
+ RM = Slider( axRM, 'RM ( ohm.m^2 )', 0.1, 10, valinit=1.0 )
+ CM = Slider( axCM, 'CM ( Farad/m^2)', 0.001, 0.1, valinit=0.01 )
+ RA = Slider( axRA, 'RA ( ohm.m', 0.1, 10, valinit=1.0 )
+ length = Slider( axLen, 'Total length of cell (mm)', 0.1, 10, valinit=2.0 )
+ dia = Slider( axDia, 'Diameter of cell (um)', 0.1, 10, valinit=1.0 )
+ def resetParms( event ):
+ RM.reset()
+ CM.reset()
+ RA.reset()
+ length.reset()
+ dia.reset()
+
+
+ stim.on_clicked( stimObj.click )
+ reset.on_clicked( resetParms )
+ q.on_clicked( doQuit )
+ RM.on_changed( updateRM )
+ CM.on_changed( updateCM )
+ RA.on_changed( updateRA )
+ length.on_changed( updateLen )
+ dia.on_changed( updateDia )
+ plt.tight_layout()
+
+ updateDisplay()
+ plt.show()
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main()
diff --git a/moose-examples/tutorials/Electrophys/ephys2_Rall_law.py b/moose-examples/tutorials/Electrophys/ephys2_Rall_law.py
new file mode 100644
index 00000000..a5f6e90d
--- /dev/null
+++ b/moose-examples/tutorials/Electrophys/ephys2_Rall_law.py
@@ -0,0 +1,268 @@
+########################################################################
+# This example demonstrates a cable
+# Copyright (C) Upinder S. Bhalla NCBS 2018
+# Released under the terms of the GNU Public License V3.
+########################################################################
+import moose
+import matplotlib.pyplot as plt
+import matplotlib.image as mpimg
+from matplotlib.widgets import Slider, Button
+import numpy as np
+import rdesigneur as rd
+
+numDendSeg = 10 # Applies both to dend and to branches.
+interval1 = 0.010
+interval2 = 0.05 - interval1
+lines = []
+# These 5 params vary only for the branches.
+RM = 1.0
+RA = 1.0
+CM = 0.01
+length = 0.001
+dia = 2e-6
+# The params below are fixed, apply to the soma and dend.
+dendRM = 2.0
+dendRA = 1.5
+dendCM = 0.02
+dendLength = 0.001
+dendDia = 2e-6
+
+# Stimulus in Amps applied to soma.
+stimStr = "2e-10"
+
+class lineWrapper():
+ def __init__( self ):
+ self.YdendLines = 0
+ self.Ybranch1Lines = 0
+ self.Ybranch2Lines = 0
+ self.CylLines = 0
+
+def makeYmodel():
+ segLen = dendLength / numDendSeg
+ rdes = rd.rdesigneur(
+ stealCellFromLibrary = True,
+ verbose = False,
+ # cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
+ # The numerical arguments are all optional
+ cellProto =
+ [['ballAndStick', 'cellBase', dendDia, segLen, dendDia, dendLength, numDendSeg]],
+ passiveDistrib = [[ '#', 'RM', str(dendRM), 'CM', str(dendCM), 'RA', str(dendRA) ]],
+ stimList = [['soma', '1', '.', 'inject', stimStr ]],
+ )
+ # Build the arms of the Y for a branching cell.
+ pa = moose.element( '/library/cellBase' )
+ x = length
+ y = 0.0
+ dx = length / ( numDendSeg * np.sqrt(2.0) )
+ dy = 0.0
+ prevc1 = moose.element( '/library/cellBase/dend{}'.format( numDendSeg-1 ) )
+ prevc2 = prevc1
+ for i in range( numDendSeg ):
+ c1 = rd.buildCompt( pa, 'branch1_{}'.format(i), RM = RM, CM = CM, RA = RA, dia = dia, x=x, y=y, dx = dx, dy = dy )
+ c2 = rd.buildCompt( pa, 'branch2_{}'.format(i), RM = RM, CM = CM, RA = RA, dia = dia, x=x, y=-y, dx = dx, dy = -dy )
+ moose.connect( prevc1, 'axial', c1, 'raxial' )
+ moose.connect( prevc2, 'axial', c2, 'raxial' )
+ prevc1 = c1
+ prevc2 = c2
+ x += dx
+ y += dy
+ rdes.buildModel()
+
+def makeCylModel():
+ segLen = dendLength / numDendSeg
+ rdes = rd.rdesigneur(
+ stealCellFromLibrary = True,
+ verbose = False,
+ # cellProto syntax: ['ballAndStick', 'name', somaDia, somaLength, dendDia, dendLength, numDendSegments ]
+ # The numerical arguments are all optional
+ cellProto =
+ [['ballAndStick', 'soma', dendDia, segLen, dendDia, 2*dendLength, 2*numDendSeg]],
+ passiveDistrib = [[ '#', 'RM', str(dendRM), 'CM', str(dendCM), 'RA', str(dendRA) ]],
+ stimList = [['soma', '1', '.', 'inject', stimStr ]],
+ )
+ rdes.buildModel()
+
+def main():
+ global vec
+ makeDisplay()
+ quit()
+
+def updateRM(RM_):
+ global RM
+ RM = RM_
+ updateDisplay()
+
+def updateCM(CM_):
+ global CM
+ CM = CM_
+ updateDisplay()
+
+def updateRA(RA_):
+ global RA
+ RA = RA_
+ updateDisplay()
+
+def updateLen(val): # This does the length of the entire cell.
+ global length
+ length = val * 0.001
+ updateDisplay()
+
+def updateDia(val):
+ global dia
+ dia = val * 1e-6
+ updateDisplay()
+
+class stimToggle():
+ def __init__( self, toggle, ax ):
+ self.duration = 1
+ self.toggle = toggle
+ self.ax = ax
+
+ def click( self, event ):
+ global stimStr
+ if self.duration < 0.5:
+ self.duration = 1.0
+ self.toggle.label.set_text( "Long Stim" )
+ self.toggle.color = "yellow"
+ self.toggle.hovercolor = "yellow"
+ stimStr = "2e-10"
+ else:
+ self.duration = 0.001
+ self.toggle.label.set_text( "Short Stim" )
+ self.toggle.color = "orange"
+ self.toggle.hovercolor = "orange"
+ stimStr = "40e-9*(t<0.001)-36e-9*(t>0.001&&t<0.002)"
+ updateDisplay()
+ #self.ax.update()
+ #self.ax.redraw_in_frame()
+ #self.ax.draw()
+
+def printSomaVm():
+ print("This is somaVm" )
+
+def updateDisplay():
+ makeCylModel()
+ moose.element( '/model/elec/' ).name = 'Cyl'
+ moose.element( '/model' ).name = 'model1'
+ makeYmodel()
+ moose.element( '/model/elec/' ).name = 'Y'
+ moose.move( '/model1/Cyl', '/model' )
+ #moose.le( '/model/Y' )
+ #print "################################################"
+ #moose.le( '/model/Cyl' )
+ vecYdend = moose.wildcardFind( '/model/Y/soma,/model/Y/dend#' )
+ vecYbranch1 = moose.wildcardFind( '/model/Y/branch1#' )
+ vecYbranch2 = moose.wildcardFind( '/model/Y/branch2#' )
+ vecCyl = moose.wildcardFind( '/model/Cyl/#[ISA=CompartmentBase]' )
+ #vec[0].inject = 1e-10
+ moose.reinit()
+ dt = interval1
+ for i in lines:
+ moose.start( dt )
+ #print( len(vecCyl), len(vecYdend), len(vecYbranch1), len(vecYbranch2) )
+ i.CylLines.set_ydata( [v.Vm*1000 for v in vecCyl] )
+ i.YdendLines.set_ydata( [v.Vm*1000 for v in vecYdend] )
+ i.Ybranch1Lines.set_ydata( [v.Vm*1000 for v in vecYbranch1] )
+ i.Ybranch2Lines.set_ydata( [v.Vm*1000 for v in vecYbranch2] )
+ dt = interval2
+
+ moose.delete( '/model' )
+ moose.delete( '/model1' )
+ moose.delete( '/library' )
+ # Put in something here for the time-series on soma
+
+def doQuit( event ):
+ cylLength = 2*dendLength*float(2*numDendSeg+1)/(2*numDendSeg)
+ print( "The cylinder parameters were:\n"
+ "Length = {} microns\n"
+ "Diameter = {} microns\n"
+ "RM = {} Ohms.m^2\n"
+ "RA = {} Ohms.m\n"
+ "CM = {} Farads/m^2\n"
+ "Your branch parameters were:\n"
+ "Length = {:.2f} microns\n"
+ "Diameter = {:.2f} microns\n"
+ "RM = {:.2f} Ohms.m^2\n"
+ "RA = {:.2f} Ohms.m\n"
+ "CM = {:.3f} Farads/m^2\n".format(
+ cylLength*1e6, dendDia*1e6, dendRM, dendRA, dendCM,
+ length*1e6, dia*1e6, RM, RA, CM ) )
+ print( "The branch point was at 1100 microns from the left" )
+
+ quit()
+
+def makeDisplay():
+ global lines
+ #img = mpimg.imread( 'CableEquivCkt.png' )
+ img = mpimg.imread( 'RallsLaw.png' )
+ #plt.ion()
+ fig = plt.figure( figsize=(10,12) )
+ png = fig.add_subplot(311)
+ imgplot = plt.imshow( img )
+ plt.axis('off')
+ ax2 = fig.add_subplot(312)
+ #ax.set_ylim( 0, 0.1 )
+ plt.ylabel( 'Vm (mV)' )
+ plt.ylim( -70, 0.0 )
+ plt.xlabel( 'Position (microns)' )
+ #ax2.autoscale( enable = True, axis = 'y' )
+ plt.title( "Membrane potential as a function of position along cell." )
+ #for i,col in zip( range( 5 ), ['k', 'b', 'g', 'y', 'm' ] ):
+ for i,col in zip( range( 2 ), ['b', 'k' ] ):
+ lw = lineWrapper()
+ lw.YdendLines, = ax2.plot( np.arange(0, numDendSeg+1, 1 ),
+ np.zeros(numDendSeg+1), col + '.' )
+ lw.Ybranch1Lines, = ax2.plot( np.arange(0, numDendSeg, 1) + numDendSeg + 1,
+ np.zeros(numDendSeg), col + ':' )
+ lw.Ybranch2Lines, = ax2.plot( np.arange(0, numDendSeg, 1) + numDendSeg + 1,
+ np.zeros(numDendSeg) + numDendSeg + 1, col + '.' )
+ lw.CylLines, = ax2.plot( np.arange(0, numDendSeg*2+1, 1),
+ np.zeros(numDendSeg*2+1), 'r-' )
+ lines.append( lw )
+
+ ax = fig.add_subplot(313)
+ plt.axis('off')
+ axcolor = 'palegreen'
+ axStim = plt.axes( [0.02,0.05, 0.20,0.03], facecolor='green' )
+ axReset = plt.axes( [0.25,0.05, 0.30,0.03], facecolor='blue' )
+ axQuit = plt.axes( [0.60,0.05, 0.30,0.03], facecolor='blue' )
+ axRM = plt.axes( [0.25,0.1, 0.65,0.03], facecolor=axcolor )
+ axCM = plt.axes( [0.25,0.15, 0.65,0.03], facecolor=axcolor )
+ axRA = plt.axes( [0.25,0.20, 0.65,0.03], facecolor=axcolor )
+ axLen = plt.axes( [0.25,0.25, 0.65,0.03], facecolor=axcolor )
+ axDia = plt.axes( [0.25,0.30, 0.65,0.03], facecolor=axcolor )
+ #aInit = Slider( axAinit, 'A init conc', 0, 10, valinit=1.0, valstep=0.2)
+ stim = Button( axStim, 'Long Stim', color = 'yellow' )
+ stimObj = stimToggle( stim, axStim )
+
+ reset = Button( axReset, 'Reset', color = 'cyan' )
+ q = Button( axQuit, 'Quit', color = 'pink' )
+ RM = Slider( axRM, 'RM ( ohm.m^2 )', 0.1, 10, valinit=1.0 )
+ CM = Slider( axCM, 'CM ( Farad/m^2)', 0.001, 0.05, valinit=0.01, valfmt = '%0.3f' )
+ RA = Slider( axRA, 'RA ( ohm.m', 0.1, 10, valinit=1.0 )
+ length = Slider( axLen, 'Length of branches (mm)', 0.1, 10, valinit=2.0 )
+ dia = Slider( axDia, 'Diameter of branches (um)', 0.1, 10, valinit=1.0 )
+ def resetParms( event ):
+ RM.reset()
+ CM.reset()
+ RA.reset()
+ length.reset()
+ dia.reset()
+
+
+ stim.on_clicked( stimObj.click )
+ reset.on_clicked( resetParms )
+ q.on_clicked( doQuit )
+ RM.on_changed( updateRM )
+ CM.on_changed( updateCM )
+ RA.on_changed( updateRA )
+ length.on_changed( updateLen )
+ dia.on_changed( updateDia )
+
+ updateDisplay()
+
+ plt.show()
+
+# Run the 'main' if this script is executed standalone.
+if __name__ == '__main__':
+ main()
diff --git a/moose-examples/tutorials/Rdesigneur/README.txt b/moose-examples/tutorials/Rdesigneur/README.txt
index b64d89a9..e7684568 100644
--- a/moose-examples/tutorials/Rdesigneur/README.txt
+++ b/moose-examples/tutorials/Rdesigneur/README.txt
@@ -291,6 +291,16 @@ ex9.2_spines_in_neuronal_morpho.py: Add spines to a neuron built from a
- See if you can deliver the current injection to the spine. Hint: the
name of the spine compartments is 'head#' where # is the index of the
spine.
+
+
+ex9.3_spiral_spines.py: Just for fun. Illustrates how to place spines in a
+spiral around the dendrite. For good measure the spines get bigger the further
+they are from the soma. Note that the uniform spacing of spines is signified
+by the negative minSpacing term, the fourth argument to spineDistrib.
+ Suggestions:
+ - Play with expressions for spine size and angular placement.
+ - See what happens if the segment size gets smaller than the
+ spine spacing.
To come:
rdes_ex10.py: Build a spiny neuron, and insert the oscillatory chemical model
diff --git a/moose-examples/tutorials/Rdesigneur/ex3.2_squid_axon_propgn.py b/moose-examples/tutorials/Rdesigneur/ex3.2_squid_axon_propgn.py
index 9729a0d6..cb3e0a55 100644
--- a/moose-examples/tutorials/Rdesigneur/ex3.2_squid_axon_propgn.py
+++ b/moose-examples/tutorials/Rdesigneur/ex3.2_squid_axon_propgn.py
@@ -43,7 +43,7 @@ rdes = rd.rdesigneur(
chanDistrib = [
['Na', '#', 'Gbar', '1200' ],
['K', '#', 'Gbar', '360' ]],
- stimList = [['soma', '1', '.', 'inject', '(t>0.01 && t<0.2) * 2e-11' ]],
+ stimList = [['soma', '1', '.', 'inject', '(t>0.005 && t<0.2) * 2e-11' ]],
plotList = [['soma', '1', '.', 'Vm', 'Membrane potential']],
moogList = [['#', '1', '.', 'Vm', 'Vm (mV)']]
)
@@ -51,4 +51,4 @@ rdes = rd.rdesigneur(
rdes.buildModel()
moose.reinit()
-rdes.displayMoogli( 0.00005, 0.05, 0.0 )
+rdes.displayMoogli( 0.00005, 0.04, 0.0 )
diff --git a/moose-examples/tutorials/Rdesigneur/ex3.3_AP_collision.py b/moose-examples/tutorials/Rdesigneur/ex3.3_AP_collision.py
index b6a8ce2a..dfe4e8cd 100644
--- a/moose-examples/tutorials/Rdesigneur/ex3.3_AP_collision.py
+++ b/moose-examples/tutorials/Rdesigneur/ex3.3_AP_collision.py
@@ -52,4 +52,4 @@ rdes = rd.rdesigneur(
rdes.buildModel()
moose.reinit()
-rdes.displayMoogli( 0.00005, 0.05, 0.0 )
+rdes.displayMoogli( 0.00005, 0.03, 0.0 )
diff --git a/moose-examples/tutorials/Rdesigneur/ex3.4_myelinated_axon.py b/moose-examples/tutorials/Rdesigneur/ex3.4_myelinated_axon.py
index e91f7898..c609529d 100644
--- a/moose-examples/tutorials/Rdesigneur/ex3.4_myelinated_axon.py
+++ b/moose-examples/tutorials/Rdesigneur/ex3.4_myelinated_axon.py
@@ -58,12 +58,6 @@ rdes = rd.rdesigneur(
moogList = [['#', '1', '.', 'Vm', 'Vm (mV)']]
)
-
rdes.buildModel()
-
-for i in moose.wildcardFind( "/model/elec/#/Na" ):
- print(i.parent.name, i.Gbar)
-
moose.reinit()
-
rdes.displayMoogli( 0.00005, 0.05, 0.0 )
diff --git a/moose-examples/tutorials/Rdesigneur/ex7.2_CICR.py b/moose-examples/tutorials/Rdesigneur/ex7.2_CICR.py
index a44e4a1a..38447a8d 100644
--- a/moose-examples/tutorials/Rdesigneur/ex7.2_CICR.py
+++ b/moose-examples/tutorials/Rdesigneur/ex7.2_CICR.py
@@ -15,6 +15,7 @@ rdes = rd.rdesigneur(
turnOffElec = True,
chemDt = 0.005,
chemPlotDt = 0.02,
+ numWaveFrames = 200,
diffusionLength = 1e-6,
useGssa = False,
addSomaChemCompt = False,
diff --git a/moose-examples/tutorials/Rdesigneur/ex9.3_spiral_spines.py b/moose-examples/tutorials/Rdesigneur/ex9.3_spiral_spines.py
new file mode 100644
index 00000000..fe5c39c5
--- /dev/null
+++ b/moose-examples/tutorials/Rdesigneur/ex9.3_spiral_spines.py
@@ -0,0 +1,19 @@
+##########################################################################
+# This illustrates some of the capabilities for spine placement.
+# It has spines whose size increase with distance from the soma.
+# Further, the angular direction of the spines spirals around the dendrite.
+##########################################################################
+import moose
+import rdesigneur as rd
+rdes = rd.rdesigneur(
+ cellProto = [['ballAndStick', 'elec', 10e-6, 10e-6, 2e-6, 300e-6, 50]],
+ spineProto = [['makePassiveSpine()', 'spine']],
+ spineDistrib = [['spine', '#dend#', '3e-6', '-1e-6', '1+p*2e4', '0', 'p*6.28e7', '0']],
+ stimList = [['soma', '1', '.', 'inject', '(t>0.02) * 1e-9' ]],
+ moogList = [['#', '1', '.', 'Vm', 'Soma potential']]
+)
+
+rdes.buildModel()
+
+moose.reinit()
+rdes.displayMoogli( 0.0002, 0.025, 0.02 )
diff --git a/moose-gui/objectedit.py b/moose-gui/objectedit.py
index cbc8c22b..d5d66b60 100644
--- a/moose-gui/objectedit.py
+++ b/moose-gui/objectedit.py
@@ -175,10 +175,14 @@ class ObjectEditModel(QtCore.QAbstractTableModel):
self.fields.append(fieldName)
#harsha: For signalling models will be pulling out notes field from Annotator
# can updates if exist for other types also
- if ( isinstance(self.mooseObject, moose.PoolBase)
- or isinstance(self.mooseObject,moose.EnzBase)
- or isinstance(self.mooseObject,moose.Neutral)) :
- self.fields.append("Color")
+ if (isinstance (self.mooseObject,moose.ChemCompt) or \
+ isinstance(self.mooseObject,moose.ReacBase) or \
+ isinstance(moose.element(moose.element(self.mooseObject).parent),moose.EnzBase) \
+ ):
+ pass
+ else:
+ self.fields.append("Color")
+
flag = QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEditable
self.fieldFlags[fieldName] = flag
diff --git a/moose-gui/plugins/kkit.py b/moose-gui/plugins/kkit.py
index 4870a71d..3cd531bb 100644
--- a/moose-gui/plugins/kkit.py
+++ b/moose-gui/plugins/kkit.py
@@ -6,13 +6,14 @@ __version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Sep 7 2018"
+__updated__ = "Sep 11 2018"
#Change log:
# 2018
-#Jun 18: update the color of the group from objecteditor
+#sep 11: comparment size is calculated based on group sceneBoundingRect size
#Sep 07: in positionChange all the group's boundingRect is calculated
# and when group is moved the children's position are stored
+#Jun 18: update the color of the group from objecteditor
#code
import math
@@ -908,7 +909,16 @@ class KineticsWidget(EditorWidgetBase):
# rectcompt = calculateChildBoundingRect(grpcompt)
rectgrp = calculateChildBoundingRect(v)
v.setRect(rectgrp.x()-10,rectgrp.y()-10,(rectgrp.width()+20),(rectgrp.height()+20))
-
+ for k, v in self.qGraCompt.items():
+ #rectcompt = v.childrenBoundingRect()
+ rectcompt = calculateChildBoundingRect(v)
+ comptBoundingRect = v.boundingRect()
+ if not comptBoundingRect.contains(rectcompt):
+ self.updateCompartmentSize(v)
+
+ else:
+ rectcompt = calculateChildBoundingRect(v)
+ v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
else:
mobj = self.mooseId_GObj[element(mooseObject)]
self.updateArrow(mobj)
@@ -938,11 +948,11 @@ class KineticsWidget(EditorWidgetBase):
comptBoundingRect = v.boundingRect()
if not comptBoundingRect.contains(rectcompt):
self.updateCompartmentSize(v)
+
else:
rectcompt = calculateChildBoundingRect(v)
v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
- pass
-
+
def updateGrpSize(self,grp):
compartmentBoundary = grp.rect()
diff --git a/moose-gui/plugins/kkitUtil.py b/moose-gui/plugins/kkitUtil.py
index 71859880..b7dde1b7 100644
--- a/moose-gui/plugins/kkitUtil.py
+++ b/moose-gui/plugins/kkitUtil.py
@@ -5,12 +5,16 @@ __version__ = "1.0.0"
__maintainer__ = "HarshaRani"
__email__ = "hrani@ncbs.res.in"
__status__ = "Development"
-__updated__ = "Oct 18 2017"
+__updated__ = "Sep 17 2018"
'''
+2018
+Sep 17: when vertical or horizontal layout is applied for group, compartment size is recalculated
+Sep 11: group size is calculated based on sceneBoundingRect for compartment size
+2017
Oct 18 some of the function moved to this file from kkitOrdinateUtils
'''
-from moose import Annotator,element
+from moose import Annotator,element,ChemCompt
from kkitQGraphics import PoolItem, ReacItem,EnzItem,CplxItem,GRPItem,ComptItem
from PyQt4 import QtCore,QtGui,QtSvg
from PyQt4.QtGui import QColor
@@ -127,9 +131,10 @@ def moveX(reference, collider, layoutPt, margin):
layoutPt.drawLine_arrow(itemignoreZooming=False)
def handleCollisions(compartments, moveCallback, layoutPt,margin = 5.0):
-
+ print " handelCollision"
if len(compartments) is 0 : return
compartments = sorted(compartments, key = lambda c: c.sceneBoundingRect().center().x())
+ print " compartment ",compartments
reference = compartments.pop(0);
print (reference.name)
referenceRect = reference.sceneBoundingRect()
@@ -138,6 +143,18 @@ def handleCollisions(compartments, moveCallback, layoutPt,margin = 5.0):
)
for collider in colliders:
moveCallback(reference, collider, layoutPt,margin)
+ #print (reference.mobj).parent
+ if isinstance(element(((reference.mobj).parent)),ChemCompt):
+ v = layoutPt.qGraCompt[element(((reference.mobj).parent))]
+ #layoutPt.updateCompartmentSize(x)
+ rectcompt = calculateChildBoundingRect(v)
+ comptBoundingRect = v.boundingRect()
+ if not comptBoundingRect.contains(rectcompt):
+ layoutPt.updateCompartmentSize(v)
+
+ else:
+ rectcompt = calculateChildBoundingRect(v)
+ v.setRect(rectcompt.x()-10,rectcompt.y()-10,(rectcompt.width()+20),(rectcompt.height()+20))
return handleCollisions(compartments, moveCallback, layoutPt,margin)
def calculateChildBoundingRect(compt):
@@ -149,7 +166,6 @@ def calculateChildBoundingRect(compt):
ypos = []
xpos = []
for l in compt.childItems():
-
''' All the children including pool,reac,enz,polygon(arrow),table '''
if not isinstance(l,QtSvg.QGraphicsSvgItem):
if (not isinstance(l,QtGui.QGraphicsPolygonItem)):
@@ -158,11 +174,18 @@ def calculateChildBoundingRect(compt):
xpos.append(l.pos().x())
ypos.append(l.pos().y()+l.boundingRect().bottomRight().y())
ypos.append(l.pos().y())
+
else:
+ xpos.append(l.sceneBoundingRect().x())
+ xpos.append(l.sceneBoundingRect().bottomRight().x())
+ ypos.append(l.sceneBoundingRect().y())
+ ypos.append(l.sceneBoundingRect().bottomRight().y())
+ '''
xpos.append(l.rect().x())
xpos.append(l.boundingRect().bottomRight().x())
ypos.append(l.rect().y())
ypos.append(l.boundingRect().bottomRight().y())
+ '''
if (isinstance(l,PoolItem) or isinstance(l,EnzItem)):
''' For Enz cplx height and for pool function height needs to be taken'''
for ll in l.childItems():
diff --git a/moose-gui/plugins/kkitViewcontrol.py b/moose-gui/plugins/kkitViewcontrol.py
index a813bffe..06fa8b7f 100644
--- a/moose-gui/plugins/kkitViewcontrol.py
+++ b/moose-gui/plugins/kkitViewcontrol.py
@@ -144,13 +144,14 @@ class GraphicalView(QtGui.QGraphicsView):
elif gsolution[1] == GROUP_INTERIOR:
groupInteriorfound = True
groupList.append(gsolution)
-
if item.name == COMPARTMENT:
csolution = (item, self.resolveCompartmentInteriorAndBoundary(item, position))
if csolution[1] == COMPARTMENT_BOUNDARY:
- comptInteriorfound = True
- comptBoundary.append(csolution)
-
+ return csolution
+ # elif csolution[1] == COMPARTMENT_INTERIOR:
+ # comptInteriorfound = True
+ # comptBoundary.append(csolution)
+
if groupInteriorfound:
if comptInteriorfound:
return comptBoundary[0]
@@ -181,7 +182,6 @@ class GraphicalView(QtGui.QGraphicsView):
##This is kept for reference, so that if object (P,R,E,Tab,Fun) is moved outside the compartment,
#then it need to be pull back to original position
self.state["press"]["scenepos"] = item.parent().scenePos()
-
if itemType == COMPARTMENT_INTERIOR or itemType == GROUP_BOUNDARY or itemType == GROUP_INTERIOR:
self.removeConnector()
@@ -194,6 +194,9 @@ class GraphicalView(QtGui.QGraphicsView):
if itemType == GROUP_BOUNDARY:
popupmenu = QtGui.QMenu('PopupMenu', self)
popupmenu.addAction("DeleteGroup", lambda : self.deleteGroup(item,self.layoutPt))
+ popupmenu.addAction("LinearLayout", lambda : handleCollisions(list(self.layoutPt.qGraGrp.values()), moveX, self.layoutPt))
+ popupmenu.addAction("VerticalLayout" ,lambda : handleCollisions(list(self.layoutPt.qGraGrp.values()), moveMin, self.layoutPt ))
+
#popupmenu.addAction("CloneGroup" ,lambda : handleCollisions(comptList, moveMin, self.layoutPt ))
popupmenu.exec_(self.mapToGlobal(event.pos()))
@@ -361,6 +364,12 @@ class GraphicalView(QtGui.QGraphicsView):
grpCmpt = self.findGraphic_groupcompt(item)
if movedGraphObj.parentItem() != grpCmpt:
'''Not same compartment/group to which it belonged to '''
+ if isinstance(movedGraphObj,FuncItem):
+ funcPool = moose.element((movedGraphObj.mobj.neighbors['valueOut'])[0])
+ parentGrapItem = self.layoutPt.mooseId_GObj[moose.element(funcPool)]
+ if parentGrapItem.parentItem() != grpCmpt:
+ self.objectpullback("Functionparent",grpCmpt,movedGraphObj,xx,yy)
+
if isinstance(movedGraphObj,(EnzItem,MMEnzItem)):
parentPool = moose.element((movedGraphObj.mobj.neighbors['enzDest'])[0])
if isinstance(parentPool,PoolBase):
@@ -558,16 +567,21 @@ class GraphicalView(QtGui.QGraphicsView):
if messgtype.lower() == "all":
messgstr = "The object name \'{0}\' exist in \'{1}\' {2}".format(movedGraphObj.mobj.name,item.mobj.name,desObj)
elif messgtype.lower() =="enzymeparent":
- messgstr = "The Enzyme parent \'{0}\' doesn't exist in \'{2}\' {1} \n If you need to move the enzyme to {1} first parent pool needs to be moved".format(movedGraphObj.mobj.parent.name,desObj,item.mobj.name)
+ messgstr = "The Enzyme parent \'{0}\' doesn't exist in \'{2}\' {1} \n If you need to move the enzyme to {1} first move the parent pool".format(movedGraphObj.mobj.parent.name,desObj,item.mobj.name)
elif messgtype.lower() == "enzyme":
messgstr = "The Enzyme \'{0}\' already exist in \'{2}\' {1}".format(movedGraphObj.mobj.name,desObj,item.mobj.name)
elif messgtype.lower() == "empty":
messgstr = "The object can't be moved to empty space"
+ elif messgtype.lower() =="functionparent":
+ messgstr = "The Function parent \'{0}\' doesn't exist in \'{2}\' {1} \n If you need to move the function to {1} first move the parent pool".format(movedGraphObj.mobj.parent.name,desObj,item.mobj.name)
+
QtGui.QMessageBox.warning(None,'Could not move the object', messgstr )
QtGui.QApplication.setOverrideCursor(QtGui.QCursor(Qt.Qt.ArrowCursor))
def moveObjSceneParent(self,item,movedGraphObj,itempos,eventpos):
''' Scene parent object needs to be updated '''
+ if isinstance(movedGraphObj,FuncItem):
+ return
prevPar = movedGraphObj.parentItem()
movedGraphObj.setParentItem(item)
--
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