summaryrefslogtreecommitdiff
path: root/Makefile
blob: bf558eda2b647c5a29f84a6fb265af7ee7477821 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
# © 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=-march=native
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 -p
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