Zombie gone (#443)

* Added coords dumping to NSDFWriter, as static data

* Updates to version and change log for NSDFWriter

* Adding NSDF support to rdesigneur, and display capabilities for NSDF files. Preliminary implementation.

* Updates to NSDFWriter to handle model file inclusion. Fixes to ReadKkit.

* Added NSDFWriter2 class to group data saves by object blocks rather than classes.

* NSDFWriter2.cpp skeleton now working, much bug tracking later.

* Further bugfixes to NSDFWriter2, and supporting code in rdesigneur.

* Embedded files now saved as datasets, rather than annotations. Handles bigger files this way.

* Fixed NSDFWriter2 bugs: reinit bug.

* Fix for Gsolve.cpp which was using reference to legacy ZombieBufPool.

* Fixes for 3d viewer from nsdf and rdesigneur.

* Cosmetic fixes to moogul: merged views, timestamp display, frame speed etc.

* Update NSDFWriter2 to handle maps for saving obj path for uniform and static data. Updates to nsdfview and moogul to handle click-to-graph

* Moogul now uses the more feature-ful but slightly slower graphing in Vpython.

* Cleaned up syntax for nsdfview and for rdesigneur outputFileList specifiers.

Co-authored-by: bhalla <[email protected]>

Author: hrani

basecode/Eref.cpp

@@ -16,6 +16,12 @@ Eref::Eref()
 	;
 }
 
+Eref::Eref( const Eref& other )
+			: e_( other.e_ ), i_( other.i_ ), f_( other.f_ )
+{
+	;
+}
+
 Eref::Eref( Element* e, unsigned int index, unsigned int field )
 			: e_( e ), i_( index ), f_( field )
 {

basecode/Eref.h

@@ -16,6 +16,7 @@ class Eref
 
     friend ostream& operator <<( ostream& s, const Eref& e );
     Eref();
+	Eref( const Eref& other );
     Eref( Element* e, unsigned int index, unsigned int field = 0 );
 
     /**

basecode/ObjId.h

@@ -33,6 +33,12 @@ class ObjId
         ;
     }
 
+    ObjId( const ObjId& obj )
+        : id( obj.id ), dataIndex( obj.dataIndex ), fieldIndex( obj.fieldIndex )
+    {
+        ;
+    }
+
     /**
      * Creates a ObjId using specified Id and DataIndex
      */

biophysics/CompartmentBase.cpp

@@ -267,6 +267,11 @@ const Cinfo* CompartmentBase::initCinfo()
 			&CompartmentBase::setZ,
 			&CompartmentBase::getZ
 		);
+		static ValueFinfo< CompartmentBase, vector< double > > coords( "coords",
+			"Vector with all coords: [x0 y0 z0 x y z dia]",
+			&CompartmentBase::setCoords,
+			&CompartmentBase::getCoords
+		);
 
 	//////////////////////////////////////////////////////////////////
 	// DestFinfo definitions
@@ -322,6 +327,7 @@ const Cinfo* CompartmentBase::initCinfo()
 		&x,					// Value
 		&y,					// Value
 		&z,					// Value
+		&coords,			// Value
 		&injectMsg,			// DestFinfo
 		&randInject,		// DestFinfo
 		&injectMsg,			// DestFinfo
@@ -571,6 +577,28 @@ double CompartmentBase::getZ() const
 	return z_;
 }
 
+void CompartmentBase::setCoords( vector< double > value )
+{
+	if (value.size() < 7 ) {
+		cout << "Warning: CompartmentBase:setCoords. Vector size = " << value.size() << ", require 7 = [ x0 y0 z0 x y z dia ] \n";
+		return;
+	}
+	x0_ = value[0];
+	y0_ = value[1];
+	z0_ = value[2];
+	x_ = value[3];
+	y_ = value[4];
+	z_ = value[5];
+	diameter_ = value[6];
+	updateLength();
+}
+
+vector< double > CompartmentBase::getCoords() const
+{
+	vector< double > ret = { x0_, y0_, z0_, x_, y_, z_, diameter_ };
+	return ret;
+}
+
 //////////////////////////////////////////////////////////////////
 // CompartmentBase::Dest function definitions.
 //////////////////////////////////////////////////////////////////

biophysics/CompartmentBase.h

@@ -57,6 +57,8 @@ class CompartmentBase
 			double getY() const;
 			void setZ( double value );
 			double getZ() const;
+			void setCoords( vector< double > value );
+			vector< double > getCoords() const;
 
 			// Dest function definitions.
 			/**

builtins/CMakeLists.txt

@@ -74,6 +74,7 @@ if(WITH_NSDF AND HDF5_FOUND)
     list(APPEND SRCS
     HDF5WriterBase.cpp
     NSDFWriter.cpp
+    NSDFWriter2.cpp
     HDF5DataWriter.cpp
     SpikeStats.cpp
     testBuiltins.cpp

builtins/InputVariable.cpp

@@ -50,6 +50,7 @@
 #include "hdf5.h"
 
 #include "NSDFWriter.h"
+#include "NSDFWriter2.h"
 #include "InputVariable.h"
 
 
@@ -81,7 +82,7 @@ const Cinfo * InputVariable::initCinfo()
 
 static const Cinfo *InputVariableCinfo = InputVariable::initCinfo();
 
-InputVariable::InputVariable(): owner_(0)
+InputVariable::InputVariable(): owner_(0), owner2_(0)
 {
     ;
 }
@@ -96,12 +97,18 @@ void InputVariable::setOwner( NSDFWriter * owner)
     owner_ = owner;
 }
 
+void InputVariable::setOwner( NSDFWriter2 * owner)
+{
+    owner2_ = owner;
+}
+
 void InputVariable::epSetValue( const Eref& eref, double value)
 {
-    if (owner_)
-    {
+    if (owner_) {
         owner_->setInput(eref.fieldIndex(), value);
-    }
+    } else if ( owner2_ ) {
+        owner2_->setInput(eref.fieldIndex(), value);
+	}
 }
 #endif
 

builtins/InputVariable.h

@@ -52,6 +52,7 @@
 #include "Variable.h"
 
 class NSDFWriter;
+class NSDFWriter2;
 
 /**
    This class is for collecting data and updating a handler object
@@ -65,9 +66,11 @@ class InputVariable: public Variable
     ~InputVariable();
     void epSetValue(const Eref &eref, double value);
     void setOwner(NSDFWriter * owner);
+    void setOwner(NSDFWriter2 * owner);
     static const Cinfo * initCinfo();
   protected:
     NSDFWriter * owner_;
+    NSDFWriter2 * owner2_;
 };
 
 #endif

builtins/NSDFWriter.cpp

@@ -6,9 +6,9 @@
 // Maintainer:
 // Created: Thu Jun 18 23:16:11 2015 (-0400)
 // Version:
-// Last-Updated: Sun Dec 20 23:20:19 2015 (-0500)
-//           By: subha
-//     Update #: 49
+// Last-Updated: Sat Jan 29 2022
+//           By: bhalla
+//     Update #: 50
 // URL:
 // Keywords:
 // Compatibility:
@@ -22,7 +22,7 @@
 //
 
 // Change log:
-//
+// Jan 2022: Many changes added
 //
 //
 //
@@ -49,9 +49,9 @@
 #include "hdf5.h"
 #include "hdf5_hl.h"
 
+#include <fstream>
 #include <ctime>
 #include <deque>
-
 #include "../basecode/header.h"
 #include "../utility/utility.h"
 #include "../utility/strutil.h"
@@ -67,8 +67,11 @@ extern template herr_t writeScalarAttr(hid_t file_id, string path, double value)
 
 const char* const EVENTPATH = "/data/event";
 const char* const UNIFORMPATH = "/data/uniform";
+const char* const STATICPATH = "/data/static";
 const char* const MODELTREEPATH = "/model/modeltree";
+const char* const MODELFILEPATH = "/model/modelfile";
 const char* const MAPUNIFORMSRC = "/map/uniform";
+const char* const MAPSTATICSRC = "/map/static";
 const char* const MAPEVENTSRC = "/map/event";
 
 string iso_time(time_t * t)
@@ -99,10 +102,16 @@ const Cinfo * NSDFWriter::initCinfo()
 
     static ValueFinfo <NSDFWriter, string > modelRoot(
       "modelRoot",
-      "The moose element tree root to be saved under /model/modeltree",
+      "The moose element tree root to be saved under /model/modeltree. If blank, nothing is saved. Default: root object, '/'", 
       &NSDFWriter::setModelRoot,
       &NSDFWriter::getModelRoot);
 
+    static ValueFinfo <NSDFWriter, string > modelFileNames(
+      "modelFileNames",
+      "Comma separated list of model files to save into the NSDF file.",
+      &NSDFWriter::setModelFiles,
+      &NSDFWriter::getModelFiles);
+
     static DestFinfo process(
         "process",
         "Handle process calls. Collects data in buffer and if number of steps"
@@ -125,7 +134,8 @@ const Cinfo * NSDFWriter::initCinfo()
         processShared, sizeof( processShared ) / sizeof( Finfo* ));
 
     static Finfo * finfos[] = {
-        &eventInputFinfo,
+        &eventInputFinfo,	// FieldElementFinfo
+		&modelFileNames,	// ValueFinfo
         &proc,
     };
 
@@ -267,19 +277,37 @@ void NSDFWriter::openUniformData(const Eref &eref)
    create the DS for uniform data.
  */
 void NSDFWriter::createUniformMap()
+{
+	innerCreateMaps( MAPUNIFORMSRC );
+}
+
+/**
+   create the DS for static data.
+ */
+void NSDFWriter::createStaticMap()
+{
+	innerCreateMaps( MAPSTATICSRC );
+}
+
+
+/**
+   Generic call for create the DS for static/uniform data
+ */
+void NSDFWriter::innerCreateMaps( const char* const mapSrcStr )
 {
     // Create the container for all the DS
-    // TODO: make a common function like `mkdir -p` to avoid repeating this
     htri_t exists;
     herr_t status;
-    hid_t uniformMapContainer = require_group(filehandle_, MAPUNIFORMSRC);
+    hid_t uniformMapContainer = require_group(filehandle_, mapSrcStr );
     // Create the DS themselves
     for (map< string, vector < unsigned int > >::iterator ii = classFieldToSrcIndex_.begin();
          ii != classFieldToSrcIndex_.end(); ++ii){
         vector < string > pathTokens;
         moose::tokenize(ii->first, "/", pathTokens);
         string className = pathTokens[0];
         string fieldName = pathTokens[1];
+		if (mapSrcStr == MAPSTATICSRC ) //Hack. for now only static field is coords
+			fieldName = "coords";
         hid_t container = require_group(uniformMapContainer, className);
         char ** sources = (char **)calloc(ii->second.size(), sizeof(char*));
         for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
@@ -291,9 +319,6 @@ void NSDFWriter::createUniformMap()
         status = H5Tset_size(memtype, H5T_VARIABLE);
         assert(status >= 0);
         status = H5Dwrite(ds, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, sources);
-#ifndef NDEBUG
-        cout << "Write dataset: status=" << status << endl;
-#endif
         assert(status >= 0);
         for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
             free(sources[jj]);
@@ -534,9 +559,12 @@ void NSDFWriter::reinit(const Eref& eref, const ProcPtr proc)
         writeScalarAttr< double >(it->second, "dt", proc->dt);
     }
     openEventData(eref);
+    writeModelFiles();
     writeModelTree();
     createUniformMap();
+    createStaticMap();
     createEventMap();
+	writeStaticCoords();
     steps_ = 0;
 }
 
@@ -627,9 +655,97 @@ string NSDFWriter::getModelRoot() const
     return modelRoot_;
 }
 
+void NSDFWriter::setModelFiles(string value)
+{
+	modelFileNames_.clear();	
+    moose::tokenize( value, ", ", modelFileNames_);
+}
+
+string NSDFWriter::getModelFiles() const
+{
+	string ret = "";
+	string spacer = "";
+	for( auto s = modelFileNames_.begin(); s!= modelFileNames_.end(); ++s) {
+		ret += spacer + *s;
+		spacer = ",";
+	}
+    return ret;
+}
+
+void NSDFWriter::writeStaticCoords()
+{
+    hid_t staticObjContainer = require_group(filehandle_, STATICPATH );
+    for (map< string, vector < unsigned int > >::iterator ii = classFieldToSrcIndex_.begin(); ii != classFieldToSrcIndex_.end(); ++ii){
+        vector < string > pathTokens;
+        moose::tokenize(ii->first, "/", pathTokens);
+        string className = pathTokens[0];
+		string fieldName = "coords"; // pathTokens[1] is not relevant.
+        hid_t container = require_group(staticObjContainer, className);
+        double * buffer = (double*)calloc(ii->second.size() * 7, sizeof(double));
+		// Ugly class checking stuff here: Both have a coord field
+		if ( className.find( "Pool" ) != string::npos || 
+			 className.find( "Compartment" ) != string::npos ) {
+        	for (unsigned int jj = 0; jj < ii->second.size(); ++jj) {
+            	vector< double > coords = Field< vector< double > >::get( src_[ii->second[jj]], fieldName.c_str() );
+				if ( coords.size() == 11 ) { // For SpineMesh
+					for ( unsigned int kk = 0; kk < 6; ++kk) {
+						buffer[jj * 7 + kk] = coords[kk];
+					}
+					buffer[jj * 7 + 6] = coords[9]; // head Dia 
+				} else if ( coords.size() == 4 ) { // for EndoMesh
+					for ( unsigned int kk = 0; kk < 3; ++kk) {
+						buffer[jj * 7 + kk] = coords[kk];
+						buffer[jj * 7 + kk+3] = coords[kk];
+					}
+					buffer[jj * 7 + 6] = coords[3];
+				} else if ( coords.size() >= 7 ) { // For NeuroMesh
+					for ( unsigned int kk = 0; kk < 7; ++kk) {
+						buffer[jj * 7 + kk] = coords[kk];
+					}
+				}
+			}
+		} else { // Want to check for things like Ca in an elec compt...
+        	for (unsigned int jj = 0; jj < ii->second.size(); ++jj) {
+				for ( unsigned int kk = 0; kk < 7; ++kk) {
+					buffer[jj * 7 + kk] = 0.0;
+				}
+			}
+		}
+        hsize_t dims[2];
+		dims[0] = ii->second.size();
+		dims[1] = 7;
+        hid_t memspace = H5Screate_simple(2, dims, NULL);
+        hid_t dataspace = H5Screate_simple(2, dims, NULL);
+    	hid_t dataset = H5Dcreate2(container, fieldName.c_str(), H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+        hid_t filespace = H5Dget_space(dataset);
+        herr_t status = H5Dwrite(dataset, H5T_NATIVE_DOUBLE,  memspace, filespace, H5P_DEFAULT, buffer);
+		if ( status < 0 ) {
+			cout << "Error: Failed to write coords as static entry\n";
+		}
+	}
+}
+
+void NSDFWriter::writeModelFiles()
+{
+	for ( const string& fName : modelFileNames_ ) {
+    	// string fPath = MODELFILEPATH + string("/") + fName;
+    	string fPath = MODELFILEPATH;
+		std::ifstream f( fName );
+		auto ss = ostringstream{};
+		if ( f.is_open() ) {
+			ss << f.rdbuf();
+    		hid_t fGroup = require_group(filehandle_, fPath);
+    		writeScalarAttr<string>(fGroup, fName, ss.str());
+		} else {
+			cout << "Warning: NSDFWriter::writeModelFiles Could not open file '" << fName << "'/n";
+		}
+	}
+}
 
 void NSDFWriter::writeModelTree()
 {
+	if (modelRoot_ == "")
+		return;
     vector< string > tokens;
     ObjId mRoot(modelRoot_);
     string rootPath = MODELTREEPATH + string("/") + mRoot.element()->getName();