EI/VirtualLeaf Changeset - aaba9e8828d6 · Centrum Wiskunde & Informatica (CWI)

Changeset - aaba9e8828d6

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Roeland Merks - 15 years ago 2010-06-07 15:50:24
roeland.merks@cwi.nl

Added to new menu options: edit->ResetChemicals and edit->ResetTransporters, which allows you to set only the chemicals or only the transporters to the initial values. I needed this for preparing a suitable initial condition for Tutorial 6 and thought it would be useful for the main distribution.

--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
changed src/build_models/Makefile
changed src/canvas.cpp
changed src/canvas.h
changed src/mesh.cpp
changed src/mesh.h

5 files changed with 315 insertions and 59 deletions:

src/build_models/Makefile

219

src/canvas.cpp

src/canvas.h

src/mesh.cpp

src/mesh.h

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src/build_models/Makefile

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 # $Id: Makefile,v 3f0977faba37 2010/06/03 15:54:37 michael $
 #############################################################################
 # Makefile for building: libauxinsimon.so
 # Generated by qmake (2.01a) (Qt 4.4.1) on: Mon Jun 7 13:36:27 2010
 # Project:  auxinsimon.pro
 # Template: lib
 # Command: /ufs/merks/Trolltech/Qt-4.4.1/bin/qmake -unix -o Makefile auxinsimon.pro
 #############################################################################
-QMAKE = qmake
+####### Compiler, tools and options
 all: plugin_auxingrowth plugin_leaf plugin_meinhardt plugin_test
 CC            = gcc
 CXX           = g++
 DEFINES       = -DQTGRAPHICS -DQT_NO_DEBUG -DQT_PLUGIN -DQT_QT3SUPPORT_LIB -DQT3_SUPPORT -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED
 CFLAGS        = -m64 -pipe -O2 -Wall -W -D_REENTRANT -fPIC $(DEFINES)
 CXXFLAGS      = -m64 -pipe -fexceptions -I.. -fPIC -I/usr/include/libxml2 -O2 -Wall -W -D_REENTRANT -fPIC $(DEFINES)
 INCPATH       = -I../../../../Trolltech/Qt-4.4.1/mkspecs/linux-g++-64 -I. -I../../../../Trolltech/Qt-4.4.1/include/QtCore -I../../../../Trolltech/Qt-4.4.1/include/QtCore -I../../../../Trolltech/Qt-4.4.1/include/QtGui -I../../../../Trolltech/Qt-4.4.1/include/QtGui -I../../../../Trolltech/Qt-4.4.1/include/Qt3Support -I../../../../Trolltech/Qt-4.4.1/include/Qt3Support -I../../../../Trolltech/Qt-4.4.1/include -I. -I.
 LINK          = g++
 LFLAGS        = -m64 -fPIC -Wl,-rpath,/ufs/merks/Trolltech/Qt-4.4.1/lib -shared
 LIBS          = $(SUBLIBS)  -L/ufs/merks/Trolltech/Qt-4.4.1/lib -L../../lib -lvleaf -lQt3Support -L/ufs/merks/Trolltech/Qt-4.4.1/lib -lQtSql -pthread -pthread -pthread -pthread -lQtXml -pthread -pthread -pthread -pthread -L/usr/X11R6/lib64 -pthread -pthread -pthread -pthread -pthread -pthread -lQtNetwork -pthread -pthread -pthread -pthread -pthread -pthread -lQtGui -pthread -lpng -lSM -lICE -pthread -pthread -lXi -lXrender -lXrandr -lfreetype -lfontconfig -lXext -lX11 -lQtCore -lz -lm -pthread -lgthread-2.0 -lrt -lglib-2.0 -ldl -lpthread
 AR            = ar cqs
 RANLIB        =
 QMAKE         = /ufs/merks/Trolltech/Qt-4.4.1/bin/qmake
 TAR           = tar -cf
 COMPRESS      = gzip -9f
 COPY          = cp -f
 SED           = sed
 COPY_FILE     = $(COPY)
 COPY_DIR      = $(COPY) -r
 INSTALL_FILE  = install -m 644 -p
 INSTALL_DIR   = $(COPY_DIR)
 INSTALL_PROGRAM = install -m 755 -p
 DEL_FILE      = rm -f
 SYMLINK       = ln -sf
 DEL_DIR       = rmdir
 MOVE          = mv -f
 CHK_DIR_EXISTS= test -d
 MKDIR         = mkdir -p
 plugin_auxingrowth: Makefile.plugin_auxingrowth
 	make -f Makefile.plugin_auxingrowth
 ####### Output directory
 OBJECTS_DIR   = ./
 ####### Files
 Makefile.plugin_auxingrowth: plugin_auxingrowth.pro
 	$(QMAKE) -makefile -o $@ $<
 SOURCES       = auxinsimon.cpp moc_auxinsimon.cpp
 OBJECTS       = auxinsimon.o \
 		moc_auxinsimon.o
 DIST          = ../../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf \
 		auxinsimon.pro
 QMAKE_TARGET  = auxinsimon
 DESTDIR       = ../../bin/models/
 TARGET        = libauxinsimon.so
 TARGETD       = libauxinsimon.so
 plugin_leaf: Makefile.plugin_leaf
 	make -f Makefile.plugin_leaf
 first: all
 ####### Implicit rules
 .SUFFIXES: .o .c .cpp .cc .cxx .C
 .cpp.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .cc.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .cxx.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 Makefile.plugin_leaf: plugin_leaf.pro
 	$(QMAKE) -makefile -o $@ $<
 .C.o:
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o "$@" "$<"
 .c.o:
 	$(CC) -c $(CFLAGS) $(INCPATH) -o "$@" "$<"
 ####### Build rules
 all: Makefile  ../../bin/models/$(TARGET)
 ../../bin/models/$(TARGET):  $(OBJECTS) $(SUBLIBS) $(OBJCOMP)
 	@$(CHK_DIR_EXISTS) ../../bin/models/ || $(MKDIR) ../../bin/models/
 	-$(DEL_FILE) $(TARGET)
 	$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(LIBS) $(OBJCOMP)
 	-$(MOVE) $(TARGET) ../../bin/models/
 plugin_meinhardt: Makefile.plugin_meinhardt
 	make -f Makefile.plugin_meinhardt
 Makefile: auxinsimon.pro  ../../../../Trolltech/Qt-4.4.1/mkspecs/linux-g++-64/qmake.conf ../../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf \
 		../../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQt3Support.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtSql.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtCore.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtXml.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtGui.prl \
 		/ufs/merks/Trolltech/Qt-4.4.1/lib/libQtNetwork.prl
 	$(QMAKE) -unix -o Makefile auxinsimon.pro
 ../../../../Trolltech/Qt-4.4.1/mkspecs/common/g++.conf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/common/unix.conf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/common/linux.conf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/qconfig.pri:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_functions.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt_config.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/exclusive_builds.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_pre.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/release.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/default_post.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/warn_on.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/qt.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/unix/thread.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/moc.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/resources.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/uic.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/yacc.prf:
 ../../../../Trolltech/Qt-4.4.1/mkspecs/features/lex.prf:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQt3Support.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtSql.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtCore.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtXml.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtGui.prl:
 /ufs/merks/Trolltech/Qt-4.4.1/lib/libQtNetwork.prl:
 qmake:  FORCE
 	@$(QMAKE) -unix -o Makefile auxinsimon.pro
 Makefile.plugin_meinhardt: plugin_meinhardt.pro
 	$(QMAKE) -makefile -o $@ $<
 dist:
 	@$(CHK_DIR_EXISTS) .tmp/auxinsimon1.0.0 || $(MKDIR) .tmp/auxinsimon1.0.0
 	$(COPY_FILE) --parents $(SOURCES) $(DIST) .tmp/auxinsimon1.0.0/ && $(COPY_FILE) --parents ../simplugin.h auxinsimon.h .tmp/auxinsimon1.0.0/ && $(COPY_FILE) --parents auxinsimon.cpp .tmp/auxinsimon1.0.0/ && (cd `dirname .tmp/auxinsimon1.0.0` && $(TAR) auxinsimon1.0.0.tar auxinsimon1.0.0 && $(COMPRESS) auxinsimon1.0.0.tar) && $(MOVE) `dirname .tmp/auxinsimon1.0.0`/auxinsimon1.0.0.tar.gz . && $(DEL_FILE) -r .tmp/auxinsimon1.0.0
 plugin_test: Makefile.plugin_test
 	make -f Makefile.plugin_test
 clean:compiler_clean
 	-$(DEL_FILE) $(OBJECTS)
 	-$(DEL_FILE) *~ core *.core
 ####### Sub-libraries
 Makefile.plugin_test: plugin_test.pro
 	$(QMAKE) -makefile -o $@ $<
 distclean: clean
 	-$(DEL_FILE) $(TARGET)
 	-$(DEL_FILE) Makefile
 mocclean: compiler_moc_header_clean compiler_moc_source_clean
 mocables: compiler_moc_header_make_all compiler_moc_source_make_all
 compiler_moc_header_make_all: moc_auxinsimon.cpp
 compiler_moc_header_clean:
 	-$(DEL_FILE) moc_auxinsimon.cpp
 moc_auxinsimon.cpp: ../simplugin.h \
 		../cellbase.h \
 		../vector.h \
 		../sqr.h \
 		../parameter.h \
 		../wall.h \
 		../wallbase.h \
 		../warning.h \
 		auxinsimon.h
 	/ufs/merks/Trolltech/Qt-4.4.1/bin/moc $(DEFINES) $(INCPATH) auxinsimon.h -o moc_auxinsimon.cpp
 clean:
 	make -f Makefile.plugin_auxingrowth clean
 	make -f Makefile.plugin_leaf clean
 	make -f Makefile.plugin_meinhardt clean
 	make -f Makefile.plugin_test clean
 compiler_rcc_make_all:
 compiler_rcc_clean:
 compiler_image_collection_make_all: qmake_image_collection.cpp
 compiler_image_collection_clean:
 	-$(DEL_FILE) qmake_image_collection.cpp
 compiler_moc_source_make_all:
 compiler_moc_source_clean:
 compiler_uic_make_all:
 compiler_uic_clean:
 compiler_yacc_decl_make_all:
 compiler_yacc_decl_clean:
 compiler_yacc_impl_make_all:
 compiler_yacc_impl_clean:
 compiler_lex_make_all:
 compiler_lex_clean:
 compiler_clean: compiler_moc_header_clean
 ####### Compile
 #finis
 auxinsimon.o: auxinsimon.cpp ../simplugin.h \
 		../cellbase.h \
 		../vector.h \
 		../sqr.h \
 		../parameter.h \
 		../wall.h \
 		../wallbase.h \
 		../warning.h \
 		auxinsimon.h
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o auxinsimon.o auxinsimon.cpp
 moc_auxinsimon.o: moc_auxinsimon.cpp
 	$(CXX) -c $(CXXFLAGS) $(INCPATH) -o moc_auxinsimon.o moc_auxinsimon.cpp
 ####### Install
 install:   FORCE
 uninstall:   FORCE
 FORCE:

src/canvas.cpp

➞

Show inline comments

@@ @@ -562,6 +562,8 @@ Main::Main(QGraphicsScene& c, Mesh &m, Q @@
 	Q3PopupMenu* edit = new Q3PopupMenu( menu );
   edit->insertItem("Reset Chemicals and Transporters", this, SLOT( CleanMesh()), Qt::CTRL+Qt::Key_R );
 	edit->insertItem("Reset Chemicals", this, SLOT( CleanMeshChemicals()) );
 	edit->insertItem("Reset Transporters", this, SLOT( CleanMeshTransporters()) );
   edit->insertItem("Randomize PIN1 Transporters", this, SLOT( RandomizeMesh()) );
   edit->insertItem("Cut away SAM", this, SLOT( CutSAM() ));
   menu->insertItem("&Edit", edit);
@@ @@ -1437,16 +1439,58 @@ void Main::FitLeafToCanvas(void) { @@
+}
 void Main::CleanMesh(void) {
   mesh.SettoInitVals();
 	vector<double> clean_chem(Cell::NChem());
 	vector<double> clean_transporters(Cell::NChem());
 	for (int i=0;i<Cell::NChem();i++) {
 		clean_chem[i]=par.initval[i];
 		clean_transporters[i]=0.;
+	}
 	mesh.CleanChemicals(clean_chem);
 	mesh.CleanTransporters(clean_transporters);
 	mesh.setTime(0);
   Plot();
   editor->FullRedraw();
 	Plot();
 	editor->FullRedraw();
   //  repaint();
+}
 void Main::CleanMeshChemicals(void) {
 	vector<double> clean_chem(Cell::NChem());
 	for (int i=0;i<Cell::NChem();i++) {
 		clean_chem[i]=par.initval[i];
+	}
 	mesh.CleanChemicals(clean_chem);
 	mesh.setTime(0);
 	Plot();
 	editor->FullRedraw();
 	//  repaint();
+}
 void Main::CleanMeshTransporters(void) {
 	vector<double> clean_transporters(Cell::NChem());
 	for (int i=0;i<Cell::NChem();i++) {
 		clean_transporters[i]=0.;
+	}
 	mesh.CleanTransporters(clean_transporters);
 	mesh.setTime(0);
 	Plot();
 	editor->FullRedraw();
 	//  repaint();
+}
 void Main::RandomizeMesh(void) {
   vector<double> max_chem(Cell::NChem());

src/canvas.h

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Show inline comments

@@ @@ -226,8 +226,11 @@ class Main : public Q3MainWindow, public @@
   void shrink();
   void zoomIn();
   void zoomOut();
+	>
   void CleanMesh();
 	void CleanMeshChemicals(void);
 	void CleanMeshTransporters(void);
   void RandomizeMesh();
  signals:

src/mesh.cpp

➞

Show inline comments

@@ @@ -1888,35 +1888,48 @@ void Mesh::DeleteLooseWalls(void) { @@
   }*/
 void Mesh::CleanChemicals(const vector<double> &clean_chem, const vector<double> &clean_transporters) {
   if (clean_chem.size()!=(unsigned)Cell::NChem() || clean_transporters.size()!=(unsigned)Cell::NChem()) {
     throw "Run time error in Mesh::CleanChemicals: size of clean_chem and clean_transporters should be equal to Cell::NChem()";
+  }
   for (vector<Cell *>::iterator c=cells.begin();
        c!=cells.end();
        c++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*c)->SetChemical(i,clean_chem[i]);
+    }
     (*c)->SetNewChemToChem();
 void Mesh::CleanChemicals(const vector<double> &clean_chem) {
 	if (clean_chem.size()!=(unsigned)Cell::NChem()) {
 		throw "Run time error in Mesh::CleanChemicals: size of clean_chem should be equal to Cell::NChem()";
+	}
 	for (vector<Cell *>::iterator c=cells.begin();
 		 c!=cells.end();
 		 c++) {
 		for (int i=0;i<Cell::NChem();i++) {
 			(*c)->SetChemical(i,clean_chem[i]);
+		}
 		(*c)->SetNewChemToChem();
+	}
+}
+  }
 void Mesh::CleanTransporters(const vector<double> &clean_transporters) {
 	if (clean_transporters.size()!=(unsigned)Cell::NChem()) {
 		throw "Run time error in Mesh::CleanTransporters: size ofclean_transporters should be equal to Cell::NChem()";
+	}
   // clean transporters
   for (list<Wall *>::iterator w=walls.begin();
        w!=walls.end();
        w++) {
     for (int i=0;i<Cell::NChem();i++) {
       (*w)->setTransporters1(i,clean_transporters[i]); (*w)->setNewTransporters1(i,clean_transporters[i]);
       (*w)->setTransporters2(i,clean_transporters[i]); (*w)->setNewTransporters2(i,clean_transporters[i]);
+    }
+  }
 	// clean transporters
 	for (list<Wall *>::iterator w=walls.begin();
 		 w!=walls.end();
 		 w++) {
 		for (int i=0;i<Cell::NChem();i++) {
 			(*w)->setTransporters1(i,clean_transporters[i]); (*w)->setNewTransporters1(i,clean_transporters[i]);
 			(*w)->setTransporters2(i,clean_transporters[i]); (*w)->setNewTransporters2(i,clean_transporters[i]);
+		}
+	}
+}
 void Mesh::RandomizeChemicals(const vector<double> &max_chem, const vector<double> &max_transporters) {
   if (max_chem.size()!=(unsigned)Cell::NChem() || max_transporters.size()!=(unsigned)Cell::NChem()) {
@@ @@ -2158,7 +2171,8 @@ void Mesh::SettoInitVals(void) { @@
   // Amount of PIN1
   //clean_chem[1] = 0.;
   CleanChemicals(clean_chem, clean_transporters);
 	CleanChemicals(clean_chem);
 	CleanTransporters(clean_transporters);
+}

src/mesh.h

➞

Show inline comments

@@ @@ -413,7 +413,8 @@ public: @@
 		node_sets.push_back(node_set);
+	}
 	void CleanChemicals(const vector<double> &clean_chem, const vector<double> &clean_transporters);
 	void CleanChemicals(const vector<double> &clean_chem);
 	void CleanTransporters(const vector<double> &clean_transporters);
 	void RandomizeChemicals(const vector<double> &max_chem, const vector<double> &max_transporters);
 	inline double getTime(void) const { return time; }
 	string getTimeHours(void) const;

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