+#include <limits.h>

+MACHSPEC=-march=native

+MACHSTR=

+CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(OUTPUTCHOICES)

+CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(NIBRCONDITIONAL) $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(CPPTEMPWORKAROUND) $(OUTPUTCHOICES)

+COMPOPT=-O3 -p

+#COMPOPT=-g -O0 -Wall

+network.o network2D.o: network.cc network.hh Network_Statistics.hh synapse.hh synapse_formation_model.hh global.hh file.hh Command_Line_Parameters.hh Network_Generated_Statistics.hh Sampled_Output.hh Network_Statistics.hh Spatial_Segment_Subset.hh Results.hh Connection_Statistics.hh dendritic_growth_model.hh neurite_diameter_model.hh spatial.hh event.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh slice.hh

+neuron.o neuron2D.o: neuron.cc neuron.hh network.hh prepost_structure.hh connection.hh fibre_elongation_model.hh axon_direction_model.hh Color_Table.hh spatial.hh event.hh global.hh Network_Generated_Statistics.hh Sampled_Output.hh Command_Line_Parameters.hh BigString.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh

+axon_direction_model.o axon_direction_model2D.o: axon_direction_model.cc axon_direction_model.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh

+fibre_elongation_model.o fibre_elongation_model2D.o: fibre_elongation_model.cc fibre_elongation_model.hh dendritic_growth_model.hh axon_direction_model.hh fibre_structure.hh neuron.hh event.hh Command_Line_Parameters.hh global.hh diagnostic.hh

+fibre_structure.o fibre_structure2D.o: fibre_structure.cc fibre_structure.hh dendritic_growth_model.hh axon_direction_model.hh branching_models.hh fibre_elongation_model.hh environment_physics.hh neuron.hh event.hh Network_Generated_Statistics.hh Sampled_Output.hh Fig_Object.hh spatial.hh global.hh diagnostic.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh Command_Line_Parameters.hh

+prepost_structure.o prepost_structure2D.o: prepost_structure.cc prepost_structure.hh neuron.hh network.hh axon_direction_model.hh spatial.hh fibre_structure.hh Network_Generated_Statistics.hh global.hh state_storable.hh

+nibr.o nibr2D.o: nibr.cc nibr.hh network.hh synapse.hh synapse_formation_model.hh axon_direction_model.hh environment_physics.hh Command_Line_Parameters.hh Sampled_Output.hh Spatial_Presentation.hh file.hh spatial.hh event.hh slice.hh diagnostic.hh BigString.hh BigRegex.hh mtprng.hh regex-gnu.h

+ ln -s $(HOME)/src/dil2al/BigString.o

+ ln -s $(HOME)/src/dil2al/BigRegex.o

+ ln -s $(HOME)/src/dil2al/regex-gnu.o

+MACHSPEC=-march=native

+MACHSTR=

+CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(OUTPUTCHOICES)

+CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(NIBRCONDITIONAL) $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(CPPTEMPWORKAROUND) $(OUTPUTCHOICES)

+#COMPOPT=-g -O0 -Wall

+ ln -s $(HOME)/src/dil2al/BigString.o

+ ln -s $(HOME)/src/dil2al/BigRegex.o

+ ln -s $(HOME)/src/dil2al/regex-gnu.o

+# © Copyright 2008 Randal A. Koene <randalk@netmorph.org>

+#

+# With design assistance from J. van Pelt & A. van Ooyen, and support

+# from the Netherlands Organization for Scientific Research (NWO)

+# Program Computational Life Sciences grant CLS2003 (635.100.005) and

+# from the EC Marie Curie Research and Training Network (RTN)

+# NEURoVERS-it 019247.

+

+# This file is part of NETMORPH.

+

+# NETMORPH 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 of the License, or

+# (at your option) any later version.

+

+# NETMORPH 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 NETMORPH. If not, see <http://www.gnu.org/licenses/>.

+

+#

+# Makefile for NETMORPH

+# (by Randal A. Koene, randalk@minduploading.org)

+

+##########################################################

+## Compiler

+## --------

+CC=gcc

+CCPP=g++

+##########################################################

+

+INCLUDES= -I$(HOME)/src/include

+LIB_PATH= -L$(HOME)/src/lib

+

+##########################################################

+## Machine selection

+## -----------------

+## aurora (x86):

+MACHSPEC=

+MACHSTR=

+MACHOPT=

+#MACHOPT=-march=pentium4 -mtune=pentium4 -mfpmath=sse

+##

+## kenji (SUN Ultra):

+#MACHSPEC= -DSUN_RX

+#MACHSTR=SUN

+##

+##########################################################

+### Attempting a temporary fix for gcc 4.x compilation of dil2al

+### (This should be replaced by actual source code modification.)

+CPPTEMPWORKAROUND=-fno-access-control

+

+##########################################################

+## Regular Expression Library

+## --------------------------

+## (Suggestion: Using regex-gnu.h guarantees the greatest

+## amount of compatibility and identical behaviour on all

+## platforms, since it is included with the dil2al source

+## code and has been adapted for reliable use with C++.)

+##

+## regex-gnu.h adapted for integration with C++:

+GCC3FXTRA=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[3-9][.]"),-Wno-unused-function)

+ALT_REGEX=regex-gnu.o

+ALT_REGEX_H=\"regex-gnu.h\"

+MEMTESTS=

+#MEMTESTS=-DMEMTESTS

+#PROFILING=

+PROFILING=-DEVALUATE_POSSIBLE_CONNECTION_PROFILING

+#SYNAPSEINVENTORY=

+SYNAPSEINVENTORY=-DSYNAPTOGENESIS_AND_LOSS_INVENTORY

+#STATISTICSVERBOSITY=-DVERBOSE_EMPTY_DATA_SAMPLE_WARNINGS

+#STATISTICS=-DSAMPLES_INCLUDE_NETWORK_GENERATED_STATISTICS $(STATISTICSVERBOSITY)

+STATISTICS=-DSAMPLES_INCLUDE_NETWORK_STATISTICS_BASE $(STATISTICSVERBOSITY)

+#STATISTICS=-DSAMPLES_INCLUDE_NETWORK_STATISTICS_BASE

+MEMORYSAVING=

+#MEMORYSAVING=-DREDUCED_MEMORY_PTSEM

+#RNGCHOICE=-DFAST_RNG

+RNGCHOICE=-DPRECISE_RNG

+#MODELCHOICES=-DADM_PRIORITIZE_SPEED_OVER_SPACE -DTESTING_SIMPLE_ATTRACTION -DENABLE_APICAL_TUFTING_TRIGGER_DISTANCE $(RNGCHOICE) $(MEMORYSAVING) -DINCLUDE_SIMPLE_FIBER_DIAMETER

+MODELCHOICES=-DADM_PRIORITIZE_SPEED_OVER_SPACE -DTESTING_SIMPLE_ATTRACTION $(RNGCHOICE) $(MEMORYSAVING) -DINCLUDE_SIMPLE_FIBER_DIAMETER

+OUTPUTCHOICES=-DCHECK_XFIG_RANGES

+#-DTESTING_SPIKING

+#-DLEGACY_ELONGATION

+SIMULATIONMETHODS=-DENABLE_FIXED_STEP_SIMULATION -DFIXED_STEP_SIMULATION_START_AT_DT -DTESTING_SPIKING

+DEBUGGING=

+#DEBUGGING=-DDEBUG_SPHERICAL_BOUNDARY

+#DEBUGGING=-DTESTING_ELONGATION_TOTAL

+#DEBUGGING=-DTEST_FOR_NAN

+#DEBUGGING=-DINCLUDE_PDF_SAMPLING

+#-DDEBUGGING_ELONGATION -DDEBUGGING_DIRECTION -DINCLUDE_PDF_SAMPLING

+## Put conditional defines, such as -D__SPATIAL_SEGMENT_SUBSET_TEST into

+## the variable NIBRCONDITIONAL and export before running make.

+CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(OUTPUTCHOICES)

+CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(NIBRCONDITIONAL) $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA) $(MEMTESTS) $(PROFILING) $(SYNAPSEINVENTORY) $(STATISTICS) $(MODELCHOICES) $(SIMULATIONMETHODS) $(DEBUGGING) $(CPPTEMPWORKAROUND) $(OUTPUTCHOICES)

+REGEXSTR=regex-gnu_for_C++

+FIG2DEV=$(shell which fig2dev)

+##

+## rx.h:

+#ALT_REGEX=rx.o

+#ALT_REGEX_H=

+#CFXTRA= -D__DIL2AL__

+#CPPXTRA= -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP

+#REGEXSTR=rx

+##

+## generic GNU regex (Linux/GNU specific):

+#ALT_REGEX=regex.o

+#ALT_REGEX_H=regex.h

+#CFXTRA=

+#CPPXTRA= -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP

+#REGEXSTR=regex

+##

+## system <regex.h> (SUN specific):

+#ALT_REGEX=

+#ALT_REGEX_H=

+#CFXTRA= -DSYSTEM_RX

+#CPPXTRA= -D__DIL2AL__ -DSYSTEM_RX

+#REGEXSTR=system

+##########################################################

+

+##########################################################

+## Safe Regular Expressions

+## ------------------------

+## assume '\0' within String length and rm structure has

+## no sp/ep pointers:

+#SAFEREGEX=

+## make no assumptions:

+SAFEREGEX= -D_BIGREGEX_SAFE_MATCHES

+##########################################################

+

+##########################################################

+## Compiler Options

+## ----------------

+# Normal:

+COMPOPT=-O3

+OPTSTR=optimized

+## debugging information:

+# For gprof:

+#GPROF=-pg

+# For Valgrind:

+#COMPOPT=-g -O0 -Wall

+#OPTSTR=Valgrind

+# For gprof:

+#COMPOPT=-pg -O3

+#OPTSTR=Gprof

+#COMPOPT= -g

+#OPTSTR=debugging_info

+##########################################################

+

+##########################################################

+## C++ Specific Compiler Options

+## -----------------------------

+## debugging information:

+#CPPOPT=

+## generate profile information for use with gprof:

+#CPPOPT=

+## optimized:

+CPPOPT= -felide-constructors

+##########################################################

+

+CFLAGS= $(COMPOPT) $(MACHSPEC) $(CFXTRA)

+CPPFLAGS= $(COMPOPT) $(CPPOPT) $(MACHSPEC) $(CPPXTRA) $(SAFEREGEX) $(INCLUDES)

+

+.INIT:

+ @echo '-------------------------------------------------------------------'

+ @echo 'Compilation options: $(MACHSTR), $(OPTSTR), $(REGEXSTR)'

+ @echo '-------------------------------------------------------------------'

+

+all: nibr nibr2D wizard

+

+diagnostic.o: diagnostic.cc diagnostic.hh file.hh BigString.hh BigRegex.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c diagnostic.cc -o diagnostic.o

+

+state_storable.o: state_storable.cc state_storable.hh global.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c state_storable.cc -o state_storable.o

+

+mtprng.o: mtprng.cc mtprng.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c mtprng.cc -o mtprng.o

+

+global.o: global.cc global.hh file.hh Fig_Object.hh Command_Line_Parameters.hh mtprng.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c global.cc -o global.o

+

+file.o: file.cc file.hh BigString.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c file.cc -o file.o

+

+StringList.o: StringList.cc StringList.hh BigString.hh BigRegex.hh regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c StringList.cc -o StringList.o

+

+event.o event2D.o: event.cc event.hh network.hh global.hh Command_Line_Parameters.hh state_storable.hh

+ $(CCPP) $(CPPFLAGS) -DVECTOR3D -c event.cc -o event.o

+ $(CCPP) $(CPPFLAGS) -DVECTOR2D -c event.cc -o event2D.o

+

+spatial.o spatial2D.o: spatial.cc spatial.hh Spatial_Presentation.hh global.hh

+ $(CCPP) $(CPPFLAGS) -DVECTOR3D -c spatial.cc -o spatial.o

+ $(CCPP) $(CPPFLAGS) -DVECTOR2D -c spatial.cc -o spatial2D.o

+

+network.o network2D.o: network.cc network.hh Network_Statistics.hh synapse.hh synapse_formation_model.hh global.hh file.hh Command_Line_Parameters.hh Network_Generated_Statistics.hh Sampled_Output.hh Network_Statistics.hh Spatial_Segment_Subset.hh Results.hh Connection_Statistics.hh dendritic_growth_model.hh neurite_diameter_model.hh spatial.hh event.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh slice.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c network.cc -o network.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c network.cc -o network2D.o

+

+neuron.o neuron2D.o: neuron.cc neuron.hh network.hh prepost_structure.hh connection.hh fibre_elongation_model.hh axon_direction_model.hh Color_Table.hh spatial.hh event.hh global.hh Network_Generated_Statistics.hh Sampled_Output.hh Command_Line_Parameters.hh BigString.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c neuron.cc -o neuron.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c neuron.cc -o neuron2D.o

+

+IFactivity.o IFactivity2D.o: IFactivity.cc IFactivity.hh neuron.hh connection.hh Sampled_Output.hh event.hh

+ $(CCPP) $(CPPFLAGS) -DVECTOR3D -c IFactivity.cc -o IFactivity.o

+ $(CCPP) $(CPPFLAGS) -DVECTOR2D -c IFactivity.cc -o IFactivity2D.o

+

+synapse.o synapse2D.o: synapse.cc synapse.hh connection.hh synapse_structure.hh Fig_Object.hh Color_Table.hh global.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse.cc -o synapse.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse.cc -o synapse2D.o

+

+connection.o connection2D.o: connection.cc connection.hh neuron.hh Fig_Object.hh Sampled_Output.hh state_storable.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c connection.cc -o connection.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c connection.cc -o connection2D.o

+

+generic_synapse.o: generic_synapse.cc generic_synapse.hh nibr.hh BigString.hh BigRegex.hh regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c generic_synapse.cc -o generic_synapse.o

+

+synapse_formation_model.o synapse_formation_model2D.o: synapse_formation_model.cc synapse_formation_model.hh fibre_structure.hh synapse_structure.hh synapse.hh Connection_Statistics.hh neuron.hh spatial.hh Command_Line_Parameters.hh diagnostic.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse_formation_model.cc -o synapse_formation_model.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse_formation_model.cc -o synapse_formation_model2D.o

+

+branching_models.o branching_models2D.o: branching_models.cc branching_models.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c branching_models.cc -o branching_models.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c branching_models.cc -o branching_models2D.o

+

+turning_models.o turning_models2D.o: turning_models.cc turning_models.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c turning_models.cc -o turning_models.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c turning_models.cc -o turning_models2D.o

+

+axon_direction_model.o axon_direction_model2D.o: axon_direction_model.cc axon_direction_model.hh dendritic_growth_model.hh fibre_structure.hh neuron.hh spatial.hh Command_Line_Parameters.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c axon_direction_model.cc -o axon_direction_model.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c axon_direction_model.cc -o axon_direction_model2D.o

+

+fibre_elongation_model.o fibre_elongation_model2D.o: fibre_elongation_model.cc fibre_elongation_model.hh dendritic_growth_model.hh axon_direction_model.hh fibre_structure.hh neuron.hh event.hh Command_Line_Parameters.hh global.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c fibre_elongation_model.cc -o fibre_elongation_model.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c fibre_elongation_model.cc -o fibre_elongation_model2D.o

+

+dendritic_growth_model.o dendritic_growth_model2D.o: dendritic_growth_model.cc dendritic_growth_model.hh axon_direction_model.hh fibre_structure.hh network.hh neuron.hh Connection_Statistics.hh Sampled_Output.hh Command_Line_Parameters.hh global.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c dendritic_growth_model.cc -o dendritic_growth_model.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c dendritic_growth_model.cc -o dendritic_growth_model2D.o

+

+neurite_diameter_model.o: neurite_diameter_model.cc neurite_diameter_model.hh fibre_structure.hh network.hh Command_Line_Parameters.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c neurite_diameter_model.cc -o neurite_diameter_model.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c neurite_diameter_model.cc -o neurite_diameter_model2D.o

+

+environment_physics.o: environment_physics.cc environment_physics.hh neuron.hh network.hh event.hh Command_Line_Parameters.hh spatial.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c environment_physics.cc -o environment_physics.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c environment_physics.cc -o environment_physics2D.o

+

+synapse_structure.o synapse_structure2D.o: synapse_structure.cc synapse_structure.hh fibre_structure.hh Fig_Object.hh Sampled_Output.hh spatial.hh global.hh state_storable.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c synapse_structure.cc -o synapse_structure.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c synapse_structure.cc -o synapse_structure2D.o

+

+fibre_structure.o fibre_structure2D.o: fibre_structure.cc fibre_structure.hh dendritic_growth_model.hh axon_direction_model.hh branching_models.hh fibre_elongation_model.hh environment_physics.hh neuron.hh event.hh Network_Generated_Statistics.hh Sampled_Output.hh Fig_Object.hh spatial.hh global.hh diagnostic.hh state_storable.hh Txt_Object.hh VRML_Object.hh Catacomb_Object.hh Command_Line_Parameters.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c fibre_structure.cc -o fibre_structure.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c fibre_structure.cc -o fibre_structure2D.o

+

+prepost_structure.o prepost_structure2D.o: prepost_structure.cc prepost_structure.hh neuron.hh network.hh axon_direction_model.hh spatial.hh fibre_structure.hh Network_Generated_Statistics.hh global.hh state_storable.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c prepost_structure.cc -o prepost_structure.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c prepost_structure.cc -o prepost_structure2D.o

+

+Connection_Statistics.o Connection_Statistics2D.o: Connection_Statistics.cc Connection_Statistics.hh neuron.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Connection_Statistics.cc -o Connection_Statistics.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Connection_Statistics.cc -o Connection_Statistics2D.o

+

+Network_Statistics.o Network_Statistics2D.o: Network_Statistics.cc Network_Statistics.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Network_Statistics.cc -o Network_Statistics.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Network_Statistics.cc -o Network_Statistics2D.o

+

+Spatial_Segment_Subset.o Spatial_Segment_Subset2D.o: Spatial_Segment_Subset.cc Spatial_Segment_Subset.hh fibre_structure.hh synapse_formation_model.hh Fig_Object.hh Color_Table.hh spatial.hh global.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Spatial_Segment_Subset.cc -o Spatial_Segment_Subset.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Spatial_Segment_Subset.cc -o Spatial_Segment_Subset2D.o

+

+Command.o: Command.cc BigString.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Command.cc -o Command.o

+

+Command_Line_Parameters.o: Command_Line_Parameters.cc Command_Line_Parameters.hh file.hh global.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Command_Line_Parameters.cc -o Command_Line_Parameters.o

+

+Results.o: Results.cc Results.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Results.cc -o Results.o

+

+Network_Generated_Statistics.o: Network_Generated_Statistics.cc Network_Generated_Statistics.hh Command_Line_Parameters.hh global.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Network_Generated_Statistics.cc -o Network_Generated_Statistics.o

+

+Spatial_Presentation.o Spatial_Presentation2D.o: Spatial_Presentation.cc Spatial_Presentation.hh global.hh Command_Line_Parameters.hh spatial.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c Spatial_Presentation.cc -o Spatial_Presentation.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c Spatial_Presentation.cc -o Spatial_Presentation2D.o

+

+Sampled_Output.o Sampled_Output2D.o: Sampled_Output.cc Sampled_Output.hh Network_Generated_Statistics.hh Color_Table.hh Spatial_Presentation.hh Command_Line_Parameters.hh spatial.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c Sampled_Output.cc -o Sampled_Output.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c Sampled_Output.cc -o Sampled_Output2D.o

+

+Color_Table.o: Color_Table.cc Color_Table.hh Fig_Object.hh Command_Line_Parameters.hh global.hh BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Color_Table.cc -o Color_Table.o

+

+Fig_Object.o: Fig_Object.cc Fig_Object.hh BigString.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Fig_Object.cc -o Fig_Object.o

+

+Txt_Object.o: Txt_Object.cc Txt_Object.hh global.hh BigString.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c Txt_Object.cc -o Txt_Object.o

+

+VRML_Object.o: VRML_Object.cc VRML_Object.hh global.hh spatial.hh BigString.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c VRML_Object.cc -o VRML_Object.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c VRML_Object.cc -o VRML_Object2D.o

+

+Catacomb_Object.o: Catacomb_Object.cc Catacomb_Object.hh global.hh network.hh spatial.hh BigString.hh diagnostic.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c Catacomb_Object.cc -o Catacomb_Object.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c Catacomb_Object.cc -o Catacomb_Object2D.o

+

+slice.o: slice.cc slice.hh spatial.hh Command_Line_Parameters.hh global.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -c slice.cc -o slice.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -c slice.cc -o slice2D.o

+

+nibr.o nibr2D.o: nibr.cc nibr.hh network.hh synapse.hh synapse_formation_model.hh axon_direction_model.hh environment_physics.hh Command_Line_Parameters.hh Sampled_Output.hh Spatial_Presentation.hh file.hh spatial.hh event.hh slice.hh diagnostic.hh BigString.hh BigRegex.hh mtprng.hh regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR3D -DFIG2DEV=\"$(FIG2DEV)\" -c nibr.cc -o nibr.o

+ $(CCPP) $(CPPFLAGS) $(COLORS) -DVECTOR2D -DFIG2DEV=\"$(FIG2DEV)\" -c nibr.cc -o nibr2D.o

+

+wizard.o: wizard.cc wizard.hh StringList.hh BigString.hh BigRegex.hh regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c wizard.cc -o wizard.o

+

+nibr: nibr.o Txt_Object.o VRML_Object.o Catacomb_Object.o Fig_Object.o Color_Table.o Sampled_Output.o Spatial_Presentation.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset.o Network_Statistics.o Connection_Statistics.o prepost_structure.o fibre_structure.o synapse_structure.o generic_synapse.o dendritic_growth_model.o synapse_formation_model.o branching_models.o turning_models.o axon_direction_model.o fibre_elongation_model.o neurite_diameter_model.o environment_physics.o connection.o synapse.o IFactivity.o neuron.o network.o spatial.o event.o slice.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o

+ @echo "Design rule: Add only the physiology required by function."

+ @echo " ___connected neurons (connection)"

+ @echo " _____individual synapses (synapse)"

+ @echo " _______presynaptic and postsynaptic nodes and branches"

+ @echo " _________terminals, receptive zones/spines, soma, axon hillock"

+ $(CCPP) $(CPPFLAGS) nibr.o Txt_Object.o VRML_Object.o Catacomb_Object.o Fig_Object.o Color_Table.o Sampled_Output.o Spatial_Presentation.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset.o Network_Statistics.o Connection_Statistics.o prepost_structure.o fibre_structure.o synapse_structure.o generic_synapse.o dendritic_growth_model.o synapse_formation_model.o branching_models.o turning_models.o axon_direction_model.o fibre_elongation_model.o neurite_diameter_model.o environment_physics.o connection.o synapse.o IFactivity.o neuron.o network.o spatial.o event.o slice.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o -lgeometry -o netmorph $(LIB_PATH)

+ ln -f -s netmorph nibr

+

+nibr2D: nibr2D.o Txt_Object.o VRML_Object2D.o Catacomb_Object2D.o Fig_Object.o Color_Table.o Sampled_Output2D.o Spatial_Presentation2D.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset2D.o Network_Statistics2D.o Connection_Statistics2D.o prepost_structure2D.o fibre_structure2D.o synapse_structure2D.o generic_synapse.o dendritic_growth_model2D.o synapse_formation_model2D.o branching_models2D.o turning_models2D.o axon_direction_model2D.o fibre_elongation_model2D.o neurite_diameter_model2D.o environment_physics2D.o connection2D.o synapse2D.o IFactivity2D.o neuron2D.o network2D.o spatial2D.o event2D.o slice2D.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o

+ @echo "Design rule: Add only the physiology required by function."

+ @echo " ___connected neurons (connection)"

+ @echo " _____individual synapses (synapse)"

+ @echo " _______presynaptic and postsynaptic nodes and branches"

+ @echo " _________terminals, receptive zones/spines, soma, axon hillock"

+ $(CCPP) $(CPPFLAGS) nibr2D.o Txt_Object.o VRML_Object2D.o Catacomb_Object2D.o Fig_Object.o Color_Table.o Sampled_Output2D.o Spatial_Presentation2D.o Network_Generated_Statistics.o Results.o Command_Line_Parameters.o Command.o Spatial_Segment_Subset2D.o Network_Statistics2D.o Connection_Statistics2D.o prepost_structure2D.o fibre_structure2D.o synapse_structure2D.o generic_synapse.o dendritic_growth_model2D.o synapse_formation_model2D.o branching_models2D.o turning_models2D.o axon_direction_model2D.o fibre_elongation_model2D.o neurite_diameter_model2D.o environment_physics2D.o connection2D.o synapse2D.o IFactivity2D.o neuron2D.o network2D.o spatial2D.o event2D.o slice2D.o StringList.o file.o state_storable.o global.o diagnostic.o BigString.o BigRegex.o mtprng.o regex-gnu.o -lgeometry -o netmorph2D $(LIB_PATH)

+ ln -f -s netmorph2D nibr2D

+

+wizard: wizard.o StringList.o BigString.o BigRegex.o regex-gnu.o

+ $(CCPP) $(CPPFLAGS) wizard.o StringList.o BigString.o BigRegex.o regex-gnu.o -o wizard $(LIB_PATH)

+

+clean:

+ rm -r -f *.o $(NAME)

+ ln -s $(HOME)/src/dil2al/BigString.o

+ ln -s $(HOME)/src/dil2al/BigRegex.o

+ ln -s $(HOME)/src/dil2al/regex-gnu.o

+

+MACHSTR=

+GCCTUNE=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[4-9][.]"),-mtune=native)

+MACHOPT=-march=native $(GCCTUNE) -mfpmath=sse

+CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA)

+CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) $(MACHOPT) -mieee-fp -ffast-math -D_USE_ALT_REGEX -D_CPP_REGEX -DDEFAULTHOMEDIR=\"$(HOME)\" -pedantic -Wall $(GCC3FXTRA) $(CPPTEMPWORKAROUND)

+#

+# Makefile for dil2al

+# (by Randal A. Koene, randalk@minduploading.org)

+#

+# Instructions to insure a successful make:

+# 1. Insure that LIB_PATH points to the directory in which

+# -X11 and -Xext libraries can be found

+# 2. Edit the include paths (e.g. -I/usr/openwin/include) in

+# CPPFLAGS to refelect the correct location of g++, -X11

+# and -Xext include files

+# 3. Make sure the dynamic shared libraries can be located by

+# ld.so.1 at runtime (e.g. define an environment variable

+# setenv LD_LIBRARY_PATH "/usr/openwin/lib")

+

+##########################################################

+## Compiler

+## --------

+CC=gcc

+CCPP=g++

+##########################################################

+

+INCLUDES= -I$(HOME)/src/include

+

+##########################################################

+## Machine selection

+## -----------------

+## aurora (x86):

+MACHSPEC=

+MACHSTR=

+GCCTUNE=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[4-9][.]"),-mtune=native)

+#MACHOPT=

+MACHOPT=$(GCCTUNE) -mfpmath=sse

+##

+## kenji (SUN Ultra):

+#MACHSPEC= -DSUN_RX

+#MACHSTR=SUN

+##

+##########################################################

+

+### Attempting a temporary fix for gcc 4.x compilation of dil2al

+### (This should be replaced by actual source code modification.)

+CPPTEMPWORKAROUND=-fno-access-control

+RXSPECIAL=-Wno-error

+

+##########################################################

+## Regular Expression Library

+## --------------------------

+## (Suggestion: Using regex-gnu.h guarantees the greatest

+## amount of compatibility and identical behaviour on all

+## platforms, since it is included with the dil2al source

+## code and has been adapted for reliable use with C++.)

+##

+## regex-gnu.h adapted for integration with C++:

+GCC3FXTRA=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[3-9][.]"),-Wno-unused-function)

+ALT_REGEX=regex-gnu.o

+ALT_REGEX_H=\"regex-gnu.h\"

+CFXTRA= -D__DIL2AL__ -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA)

+CPPXTRA= -D__DIL2AL__ -D_ALT_REGEX_H=$(ALT_REGEX_H) $(MACHOPT) -mieee-fp -ffast-math -D_USE_ALT_REGEX -D_CPP_REGEX -DDEFAULTHOMEDIR=\"$(HOME)\" -pedantic -Wall $(GCC3FXTRA) $(CPPTEMPWORKAROUND)

+REGEXSTR=regex-gnu_for_C++

+##

+## rx.h:

+#ALT_REGEX=rx.o

+#ALT_REGEX_H=

+#CFXTRA= -D__DIL2AL__

+#CPPXTRA= -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP

+#REGEXSTR=rx

+##

+## generic GNU regex (Linux/GNU specific):

+#ALT_REGEX=regex.o

+#ALT_REGEX_H=regex.h

+#CFXTRA=

+#CPPXTRA= -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D__DIL2AL__ -D_BIGREGEX_HAS_RM_SPEP

+#REGEXSTR=regex

+##

+## system <regex.h> (SUN specific):

+#ALT_REGEX=

+#ALT_REGEX_H=

+#CFXTRA= -DSYSTEM_RX

+#CPPXTRA= -D__DIL2AL__ -DSYSTEM_RX

+#REGEXSTR=system

+##########################################################

+

+##########################################################

+## Safe Regular Expressions

+## ------------------------

+## assume '\0' within String length and rm structure has

+## no sp/ep pointers:

+#SAFEREGEX=

+## make no assumptions:

+SAFEREGEX= -D_BIGREGEX_SAFE_MATCHES

+##########################################################

+

+##########################################################

+## Compiler Options

+## ----------------

+## debugging information:

+#COMPOPT= -g

+#OPTSTR=debugging_info

+## generate profile information for use with gprof:

+#COMPOPT= -g -O6

+#OPTSTR=profiling

+## optimized:

+COMPOPT= -O3

+OPTSTR=optimized

+##########################################################

+

+##########################################################

+## C++ Specific Compiler Options

+## -----------------------------

+## debugging information:

+#CPPOPT=

+## generate profile information for use with gprof:

+#CPPOPT=

+## optimized:

+CPPOPT= -felide-constructors

+## uncomment the following optimization option only if

+## you have an older C++ compiler that does not optimize

+## return values unless explicitly told to do so with

+## the now deprecated `named return value' extension:

+#CPPOPT= $(CPPOPT) -D_USE_NAMED_RETURN_VALUE_EXTENSION

+##########################################################

+

+CFLAGS= $(COMPOPT) $(MACHSPEC) $(CFXTRA)

+CPPFLAGS= $(COMPOPT) $(CPPOPT) $(MACHSPEC) $(CPPXTRA) $(SAFEREGEX) $(INCLUDES)

+

+.INIT:

+ @echo '-------------------------------------------------------------------'

+ @echo 'Compilation options: $(MACHSTR), $(OPTSTR), $(REGEXSTR)'

+ @echo '-------------------------------------------------------------------'

+

+all: dil2al

+

+dil2al.o: dil2al.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c dil2al.cc -o dil2al.o

+

+alcomp.o: alcomp.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c alcomp.cc -o alcomp.o

+

+diladmin.o: diladmin.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c diladmin.cc -o diladmin.o

+

+utilities.o: utilities.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c utilities.cc -o utilities.o

+

+tladmin.o: tladmin.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c tladmin.cc -o tladmin.o

+

+note.o: note.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c note.cc -o note.o

+

+controller.o: controller.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c controller.cc -o controller.o

+

+tlfilter.o: tlfilter.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c tlfilter.cc -o tlfilter.o

+

+ppfilter.o: ppfilter.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c ppfilter.cc -o ppfilter.o

+

+search.o: search.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c search.cc -o search.o

+

+finances.o: finances.cc dil2al.hh BigString.hh BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c finances.cc -o finances.o

+

+cksum.o: cksum.cc cksum.hh BigString.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c cksum.cc -o cksum.o

+

+BigString.o: BigString.cc BigString.hh

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c BigString.cc -o BigString.o

+

+BigRegex.o: BigRegex.cc BigRegex.hh rx.h regex.h regex-gnu.h

+ $(CCPP) $(CPPFLAGS) $(COLORS) -c BigRegex.cc -o BigRegex.o

+

+regex.o: regex.c regex.h

+ $(CC) $(CFLAGS) -c regex.c -o regex.o

+

+regex-gnu.o: regex-gnu.c regex-gnu.h

+ $(CCPP) $(CFLAGS) -c regex-gnu.c -o regex-gnu.o

+

+rx.o: rx.c rx.h

+ $(CC) $(CFLAGS) $(COLORS) $(RXSPECIAL) -c rx.c -o rx.o

+

+dil2al: dil2al.o alcomp.o diladmin.o utilities.o tladmin.o note.o controller.o tlfilter.o ppfilter.o search.o finances.o cksum.o BigString.o BigRegex.o regex-gnu.o regex.o rx.o

+ $(CCPP) $(CPPFLAGS) dil2al.o alcomp.o diladmin.o utilities.o tladmin.o note.o controller.o tlfilter.o ppfilter.o search.o finances.o cksum.o $(ALT_REGEX) BigString.o BigRegex.o -o dil2al $(LIB_PATH)

+

+clean:

+ rm -r -f *.o $(NAME)

+

+doc++:

+ rm -r -f html

+ doc++ -d html spiker.dxx

+

+// [Update AC 201110322:] Added APICAL flag to fibre_segment

+

+ int APICAL;

+ fibre_segment(neuron & _n, fibre_segment * p, extra_fibre_data & efd): n(&_n), d(efd), parent(p), branch1(NULL), branch2(NULL), APICAL(parent->APICAL)

+ fibre_segment(neuron & _n, fibre_segment * p, extra_fibre_data & efd, Segment & s, int AP): Segment(s), n(&_n), d(efd), parent(p), branch1(NULL), branch2(NULL), APICAL(AP)

+ fibre_segment(neuron & _n, fibre_segment * p, extra_fibre_data & efd, spatial & segstart, spatial & segend): Segment(segstart,segend), n(&_n), d(efd), parent(p), branch1(NULL), branch2(NULL), APICAL(parent->APICAL)

+ fibre_segment(neuron & _n, fibre_segment * p): n(&_n), parent(p), branch1(NULL), branch2(NULL), APICAL(parent->APICAL)

+ fibre_segment(neuron & _n, fibre_segment * p, Segment & s, int AP): Segment(s), n(&_n), parent(p), branch1(NULL), branch2(NULL), APICAL(AP)

+ fibre_segment(neuron & _n, fibre_segment * p, spatial & segstart, spatial & segend): Segment(segstart,segend), n(&_n), parent(p), branch1(NULL), branch2(NULL), APICAL(parent->APICAL)

+

+ fibre_structure(neuron & _n, Segment & s, int AP): fibre_segment(_n,NULL,root_efd,s,AP), terminalsegmentsarray(NULL), terminalarraylength(0), elmodel(NULL), bmmodel(NULL), sum_l_i_cache(0.0), sum_l_i_cache_t(eq->T()), colnum(0), cache(0.0) { terminalsegments.link_before(new terminal_segment(*this,*this)); }

+

+

+ fibre_structure(neuron & _n, Segment & s, spatial & acoords, int AP): fibre_segment(_n,NULL,root_efd,s,AP), terminalsegmentsarray(NULL), terminalarraylength(0), elmodel(NULL), bmmodel(NULL), sum_l_i_cache(0.0), sum_l_i_cache_t(eq->T()), colnum(0), cache(0.0) { terminalsegments.link_before(new terminal_segment(*this,*this,acoords)); }

+

+ fibre_structure(neuron & _n, Segment & s, int AP): fibre_segment(_n,NULL,s,AP), terminalsegmentsarray(NULL), terminalarraylength(0), elmodel(NULL), bmmodel(NULL), sum_l_i_cache(0.0), sum_l_i_cache_t(eq->T()), colnum(0), cache(0.0) { terminalsegments.link_before(new terminal_segment(*this,*this)); }

+

+

+ fibre_structure(neuron & _n, Segment & s, spatial & acoords, int AP): fibre_segment(_n,NULL,s,AP), terminalsegmentsarray(NULL), terminalarraylength(0), elmodel(NULL), bmmodel(NULL), sum_l_i_cache(0.0), sum_l_i_cache_t(eq->T()), colnum(0), cache(0.0) { terminalsegments.link_before(new terminal_segment(*this,*this,acoords)); }

+MACHOPT=-march=native -mtune=native -mfpmath=sse

+CFXTRA= -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA)

+CPPXTRA= -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA)

+# Makefile for geometry classes

+# Randal A. Koene, 20050112

+

+CC=gcc

+CCPP=g++

+

+#MACHOPT=

+MACHOPT=-mtune=native -mfpmath=sse

+

+GCC3FXTRA=$(if $(shell gcc -v 2>&1 | grep "^gcc version[^0-9]*[3-9][.]"),-Wno-unused-function)

+

+CFXTRA= -DSTDC_HEADERS -pedantic -Wall -Wno-char-subscripts $(GCC3FXTRA)

+CPPXTRA= -D_ALT_REGEX_H=$(ALT_REGEX_H) -D_USE_ALT_REGEX -D_CPP_REGEX $(MACHOPT) -mieee-fp -ffast-math -pedantic -Wall $(GCC3FXTRA)

+

+COMPOPT= -O3

+CPPOPT= -felide-constructors

+

+CFLAGS= $(COMPOPT) $(CFXTRA)

+CPPFLAGS= $(COMPOPT) $(CPPOPT) $(CPPXTRA)

+

+#.c.o:

+# g++ -c -g $<

+

+#HDR = common.h point.h vector.h

+#SRC = point.c vector.c

+#OBJ = point.o vector.o

+LIB = libgeometry.a

+TAR = geometry.tar

+

+all: $(LIB)

+

+Point3D.o: Point3D.cc Point3D.hh Vector3D.hh

+ $(CCPP) $(CPPFLAGS) -c Point3D.cc -o Point3D.o

+

+Vector3D.o: Vector3D.cc Vector3D.hh Point3D.hh

+ $(CCPP) $(CPPFLAGS) -c Vector3D.cc -o Vector3D.o

+

+Point2D.o: Point2D.cc Point2D.hh Vector2D.hh

+ $(CCPP) $(CPPFLAGS) -c Point2D.cc -o Point2D.o

+

+Vector2D.o: Vector2D.cc Vector2D.hh Point2D.hh

+ $(CCPP) $(CPPFLAGS) -c Vector2D.cc -o Vector2D.o

+

+ptest: ptest.c $(LIB)

+ g++ -o ptest ptest.c $(LIB)

+

+vtest: vtest.c $(LIB)

+ g++ -o vtest vtest.c $(LIB)

+

+$(LIB): Point3D.o Vector3D.o Point2D.o Vector2D.o

+ ar rcsv $(LIB) Point3D.o Vector3D.o Point2D.o Vector2D.o

+

+tar: $(TAR)

+$(TAR): Readme Makefile *.hh *.cc

+ tar cvf $(TAR) Readme Makefile *.hh *.cc

+

+bare: clean

+ rm -f $(LIB)

+clean:

+ rm -f *.o $(TAR)

+ sed 's/MACHSTR=x86_64/#MACHSTR=x86_64/g' Makefile.linux > Makefile

+ sed 's/MACHSTR=x86_64/#MACHSTR=x86_64/g; s/^\(INCLUDES=.*\)$/\1 -I.\/mac/g' Makefile.mac > Makefile

+

+ if [ $machinespec -eq 3 ]; then

+ # Mac

+ sed 's/MACHSTR=x86_64/#MACHSTR=x86_64/g; s/^\(INCLUDES=.*\)$/\1 -I.\/mac/g' Makefile.mac > Makefile

+ fi

+

+ # in case of older versions

+if [ $machinespec -eq 3 ]; then

+ # Mac

+ sed 's/MACHSTR=x86_64/#MACHSTR=x86_64/g; s/^\(INCLUDES=.*\)$/\1 -I.\/mac/g' Makefile.mac > Makefile

+fi

+

+

+ if ((n=clp.Specifies_Parameter("warnings_on"))>=0)

+ {

+ if (downcase(clp.ParValue(n))==String("off"))

+ {

+ warnings_on = WARN_OFF;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdout"))

+ {

+ warnings_on = WARN_STDOUT;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdoutfile"))

+ {

+ warnings_on = WARN_STDOUTFILE;

+ }

+ else if (downcase(clp.ParValue(n))==String("file"))

+ {

+ warnings_on = WARN_FILE;

+ }

+ }

+ if (warnings_on>WARN_STDOUT)

+ {

+ warningfile = outputdirectory + "warnings";

+ }

+

+ if ((n=clp.Specifies_Parameter("reports_on"))>=0)

+ {

+ if (downcase(clp.ParValue(n))==String("off"))

+ {

+ reports_on = WARN_OFF;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdout"))

+ {

+ reports_on = WARN_STDOUT;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdoutfile"))

+ {

+ reports_on = WARN_STDOUTFILE;

+ }

+ else if (downcase(clp.ParValue(n))==String("file"))

+ {

+ reports_on = WARN_FILE;

+ }

+ }

+ if (reports_on>WARN_STDOUT)

+ {

+ reportfile = outputdirectory + "report";

+ }

+

+ if ((n=clp.Specifies_Parameter("progress_on"))>=0)

+ {

+ if (downcase(clp.ParValue(n))==String("off"))

+ {

+ progress_on = WARN_OFF;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdout"))

+ {

+ progress_on = WARN_STDOUT;

+ }

+ else if (downcase(clp.ParValue(n))==String("stdoutfile"))

+ {

+ progress_on = WARN_STDOUTFILE;

+ }

+ else if (downcase(clp.ParValue(n))==String("file"))

+ {

+ progress_on = WARN_FILE;

+ }

+ }

+ if (progress_on>WARN_STDOUT)

+ {

+ progressfile = outputdirectory + "progress";

+ }

+// [UPDATE AC 20110322:] Added _typeid to fibre_structure to enable distinction between Apical and Basal dendrites.

+presynaptic_structure::presynaptic_structure(neuron & _n, Segment & initseg, spatial & acoords, int _typeid): fibre_structure(_n,initseg,acoords, _typeid) {

+postsynaptic_structure::postsynaptic_structure(neuron & _n, Segment & initseg, spatial & acoords, int _typeid): fibre_structure(_n,initseg,acoords, _typeid) {

+// [Update AC 20110322:] Added include fibre_structure.hh and APICAL/BASAL flag write to .synapses file

+

+#include "fibre_structure.hh"

+ if (SynaptoGenesis_Data) (*Txt_synapselist) += String(SynaptoGenesis_Data->find_t_genesis(this),",%f");

+ if(s->DendriteSegment()->APICAL == 6)

+ {

+ (*Txt_synapselist) += String(",APICAL\n");

+ }

+ else

+ {

+ (*Txt_synapselist) += String(",BASAL\n");

+ }

+#include "file.hh"

+bool prev_conn_formed = false;

+

+double mfd = maxfibredistance[axonsegment->N()->TypeID()][dendritesegment->N()->TypeID()];

+double likelihood = -1.0;

+

+

+//"Crossing line-piece" synapse formation model:

+//A geometrical approach to synapse formation. For a detailed explanation see

+//SECO Year 2 report -- Grant agreement number 216593

+

+double dsegseg = dist3D_Segment_to_Segment(*axonsegment,*dendritesegment,s);

+

+//Initialise line-piece end points

+double Px = 0.0;

+double Py = 0.0;

+double Pz = 0.0;

+double Qx = 0.0;

+double Qy = 0.0;

+double Qz = 0.0;

+

+double Rx = 0.0;

+double Ry = 0.0;

+double Rz = 0.0;

+double Sx = 0.0;

+double Sy = 0.0;

+double Sz = 0.0;

+

+

+double px = 0.0;

+double py = 0.0;

+double pz = 0.0;

+double qx = 0.0;

+double qy = 0.0;

+double qz = 0.0;

+

+double rx = 0.0;

+double ry = 0.0;

+double rz = 0.0;

+double sx = 0.0;

+double sy = 0.0;

+double sz = 0.0;

+

+

+fibre_segment * axon_test_seg;// = axonsegment;

+fibre_segment * dendrite_test_seg;// = dendritesegment;

+

+axon_test_seg = axonsegment;

+dendrite_test_seg = dendritesegment;

+

+#ifdef VECTOR3D

+Px = axon_test_seg->P0.X();

+Py = axon_test_seg->P0.Y();

+Pz = axon_test_seg->P0.Z();

+Qx = axon_test_seg->P1.X();

+Qy = axon_test_seg->P1.Y();

+Qz = axon_test_seg->P1.Z();

+

+

+Rx = dendrite_test_seg->P0.X();

+Ry = dendrite_test_seg->P0.Y();

+Rz = dendrite_test_seg->P0.Z();

+Sx = dendrite_test_seg->P1.X();

+Sy = dendrite_test_seg->P1.Y();

+Sz = dendrite_test_seg->P1.Z();

+#endif

+

+

+

+//I

+//Perform spatial translation on axon and dendrite segments

+//Relocate segments: Express their coordinates by shifting the

+//x_0,y_0 point of the axon segment to the x=0,y=0,z=0 location.

+px = Px - Px;

+py = Py - Py;

+pz = Pz - Pz;

+qx = Qx - Px;

+qy = Qy - Py;

+qz = Qz - Pz;

+

+rx = Rx - Px;

+ry = Ry - Py;

+rz = Rz - Pz;

+sx = Sx - Px;

+sy = Sy - Py;

+sz = Sz - Pz;

+

+

+

+//II

+//First rotation: Rotate X2,Y2,Z2 coords of the axon segment into XY plane

+// Rotate X1,Y1,Z1 and X2,Y2,Z2 coords of dendrite segment accordingly

+double PQ = pow( (pow(abs(Px-Qx),2) + pow(abs(Py-Qy),2) + pow(abs(Pz-Qz),2) ), 0.5);

+double l = pow( (pow(PQ,2) - pow((Qz - Pz),2)), 0.5);

+

+

+double qx1;

+double qy1;

+double qz1;

+

+qx1 = l;

+qy1 = 0;

+qz1 = qz;

+

+double rx1;

+double ry1;

+double rz1;

+

+rx1 = ((rx*qx) + (ry*qy))/l;

+ry1 = ((-rx*qy) + (ry*qx))/l;

+rz1 = rz;

+

+double sx1;

+double sy1;

+double sz1;

+

+sx1 = ((sx*qx) + (sy*qy))/l;

+sy1 = ((-sx*qy) + (sy*qx))/l;

+sz1 = sz;

+

+

+

+//III

+//Second rotation around Y-axis of q2 onto X-axis

+

+double qx2;

+double qy2;

+double qz2;

+

+qx2 = PQ;

+qy2 = 0;

+qz2 = 0;

+

+

+double rx2;

+double ry2;

+double CR;

+double rz2;

+

+rx2 = ((rx*qx) + (ry*qy) + (rz*qz))/PQ;

+ry2 = ry1;

+CR = rx2;

+rz2 = ((-CR*qz) + (PQ*rz))/l;

+

+double sx2;

+double CS;

+double sy2;

+double sz2;

+

+sx2 = ((sx*qx)+(sy*qy)+(sz*qz))/PQ;

+CS = sx2;

+sy2 = ((-sx*qy)+(sy*qx))/l;

+sz2 = ((-CS*qz) + (PQ*sz))/l;

+

+

+

+//IV

+//Third rotation around X-axis

+

+double Or2_prime_sq;

+double Os2_prime_sq;

+

+double fv;

+

+Or2_prime_sq = pow(ry2,2) + pow(rz2,2);

+Os2_prime_sq = pow(sy2,2) + pow(sz2,2);

+fv = 0.5*( Or2_prime_sq - Os2_prime_sq )/( pow((ry2 - sy2),2) + pow((rz2 - sz2),2) ) + 0.5;

+

+

+if(abs(fv)<1e-10)

+{

+ fv = 0;

+}

+

+double Vy;

+double Vz;

+Vy = ry2 + fv*(sy2 - ry2);

+Vz = rz2 + fv*(sz2 - rz2);

+

+double lov;

+lov = pow((pow(Vy,2) + pow(Vz,2)),0.5);

+

+double rx3;

+rx3 = CR;

+

+double ry3;

+ry3 = ((ry2*Vy) +(rz2*Vz))/lov;

+

+

+double rz3;

+rz3 = ((ry2*-Vz) +(rz2*Vy))/lov;

+

+double sx3;

+sx3 = CS;

+

+double sy3;

+sy3 = ((sy2*Vy) +(sz2*Vz))/lov;

+

+double sz3;

+sz3 = ((sy2*-Vz) +(sz2*Vy))/lov;

+

+

+

+//V

+//Determine whether r3s3 intersects XY-plane

+bool CONDITION_A = false;

+bool CONDITION_B1 = false;

+bool CONDITION_B2 = false;

+if(rz3*sz3 < 0) //CONDITION A

+{

+ CONDITION_A = true;

+}

+

+

+double qx3 = PQ;

+

+

+if(rx3 > sx3) //CONDITION B1

+{

+ if(rx3 > 0 && sx3 < qx3)

+ {

+ CONDITION_B1 = true;

+ }

+}

+else if(sx3 > rx3)

+{

+ if(sx3 > 0 && rx3 < qx3)

+ {

+ CONDITION_B1 = true;

+ }

+}

+

+if(CONDITION_A == true && CONDITION_B1 ==true)

+{

+ double ux; //Interception point

+ ux = (CS*rz3 - CR*sz3)/(rz3-sz3);

+ double tx;

+

+ tx=ux;

+

+

+

+ if(ux >=0 && ux<= PQ) //Condidtion B2

+ {

+ CONDITION_B2 = true;

+ }

+

+

+ double frac_T_PQ = tx/qx;

+ double frac_U_RS = (ux - rx3)/(sx3 - rx3);

+

+ double Tx = Px + frac_T_PQ*(Qx - Px);

+ double Ty = Py + frac_T_PQ*(Qy - Py);

+ double Tz = Pz + frac_T_PQ*(Qz - Pz);

+

+ double Ux = Rx + frac_U_RS*(Sx - Rx);

+ double Uy = Ry + frac_U_RS*(Sy - Ry);

+ double Uz = Rz + frac_U_RS*(Sz - Rz);

+

+ double TU;

+ TU= pow((pow((Tx - Ux),2) + pow((Ty - Uy),2) + pow((Tz - Uz),2)),0.5);

+

+

+ if(mfd>=0.0)

+ {

+ //Set likelihood value for synapse formation between segments

+ if(CONDITION_A == true && CONDITION_B1 == true && CONDITION_B2 == true && TU <= mfd)

+ {

+ likelihood = 1.0;

+ }

+ else

+ {

+ likelihood = 0.0;

+}

+else

+{

+ likelihood = 0.0;

+}

+ }