Changeset 780


Ignore:
Timestamp:
05/14/18 17:53:10 (7 years ago)
Author:
Maciej Komosinski
Message:

Added sources for genetic encodings fB, fH, fL

Location:
cpp
Files:
22 added
5 edited

Legend:

Unmodified
Added
Removed

  • cpp/README.txt

    r775 r780  
    1616      +- canvas        - neural network layouts and drawing
    1717      +- config        - SDK elements declarations
    18       +- genetics      - genetic operators and converters between formats
     18      +- genetics      - genetic operators and converters between genetic formats
    1919         +- f1         - ...for genetic format f1 (recurrent encoding)
    2020         +- f4         - ...for genetic format f4 (developmental encoding)
    2121         +- f9         - ...for genetic format f9 (3D turtle encoding)
     22         +- fB         - ...for genetic format fB ("biological" encoding)
    2223         +- fF         - ...for genetic format fF (Foraminifera encoding)
     24         +- fH         - ...for genetic format fH (multidimensional handles)
     25         +- fL         - ...for genetic format fL (Lindenmayer systems)
    2326         +- fn         - ...for genetic format fn (numerical optimization encoding)
    2427         +- fT         - ...for genetic format fT (educational: ATGC sequences)
    … …  
    3437      +- vm            - virtual machine programming: FramScript grammar (lex and yacc/bison)
    3538          +- classes   - C++ interfaces and implementations of basic FramScript objects
    36 

  • cpp/frams/Makefile-SDK-files

    r779 r780  
    22
    33# ALL_DIRS is later expanded by the shell, no spaces/newlines allowed, or it breaks
    4 ALL_DIRS={common,frams,frams/canvas,frams/config,common/loggers,frams/genetics,frams/genetics/f0,frams/genetics/f1,frams/genetics/f2,frams/genetics/f3,frams/genetics/f4,frams/genetics/f5,frams/genetics/f6,frams/genetics/f7,frams/genetics/f8,frams/genetics/f9,frams/genetics/fn,frams/genetics/fF,frams/genetics/fT,frams/model,frams/neuro,frams/neuro/impl,frams/param,frams/test,frams/util,frams/vm/classes,common/virtfile,frams/_demos,frams/model/geometry,frams/_demos/geometry,frams/model/similarity,frams/model/similarity/SVD}
     4ALL_DIRS={common,frams,frams/canvas,frams/config,common/loggers,frams/genetics,frams/genetics/f0,frams/genetics/f1,frams/genetics/f2,frams/genetics/f3,frams/genetics/f4,frams/genetics/f5,frams/genetics/f6,frams/genetics/f7,frams/genetics/f8,frams/genetics/f9,frams/genetics/fn,frams/genetics/fF,frams/genetics/fT,frams/genetics/fB,frams/genetics/fH,frams/genetics/fL,frams/model,frams/neuro,frams/neuro/impl,frams/param,frams/test,frams/util,frams/vm/classes,common/virtfile,frams/_demos,frams/model/geometry,frams/_demos/geometry,frams/model/similarity,frams/model/similarity/SVD}
    55
    66GENMANF4=frams/genetics/f4/f4_oper.o
    … …  
    99GENMANFT=frams/genetics/fT/fTest_oper.o
    1010GENMANFN=frams/genetics/fn/fn_oper.o
     11GENMANFB=frams/genetics/fB/fB_oper.o
     12GENMANFH=frams/genetics/fH/fH_oper.o frams/genetics/fH/fH_general.o
     13GENMANFL=frams/genetics/fL/fL_oper.o frams/genetics/fL/fL_general.o frams/genetics/fL/fL_matheval.o
    1114
    1215CONVF1=frams/genetics/f1/f1_conv.o frams/genetics/geneprops.o
    … …  
    1518CONVFF=frams/genetics/fF/fF_conv.o frams/genetics/fF/fF_genotype.o frams/genetics/fF/fF_chamber3d.o
    1619CONVFN=frams/genetics/fn/fn_conv.o
     20CONVFB=frams/genetics/fB/fB_conv.o
     21CONVFH=frams/genetics/fH/fH_conv.o frams/genetics/fH/fH_general.o frams/param/mutableparam.o
     22CONVFL=frams/genetics/fL/fL_conv.o
    1723
    1824# $(sort - remove duplicates
    19 GENOCONV_SDK_OBJS=$(sort frams/genetics/defgenoconv.o frams/vm/classes/genoobj.o frams/model/autoname.o $(CONVF1) $(CONVF4) $(CONVF9) $(CONVFF) $(CONVFN))
    20 GENMAN_SDK_OBJS=$(GENMAN_COMMON_OBJS) $(GENMANF4) $(GENMANF9) $(GENMANFF) $(GENMANFT) $(GENMANFN)
     25GENOCONV_SDK_OBJS=$(sort frams/genetics/defgenoconv.o frams/vm/classes/genoobj.o frams/model/autoname.o $(CONVF1) $(CONVF4) $(CONVF9) $(CONVFF) $(CONVFN) $(CONVFB) $(CONVFH) $(CONVFL))
     26GENMAN_SDK_OBJS=$(GENMAN_COMMON_OBJS) $(GENMANF4) $(GENMANF9) $(GENMANFF) $(GENMANFT) $(GENMANFN) $(GENMANFB) $(GENMANFH) $(GENMANFL)
     27GENOCONV_AND_GENMAN_SDK_OBJS=$(sort $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS))
    2128
    2229GENMAN_COMMON_OBJS=frams/genetics/genman.o frams/param/mutableparam.o frams/param/mutparamlist.o frams/neuro/geneticneuroparam.o frams/neuro/neurolibparam.o
    … …  
    2936
    3037GENOTYPE_LOADER_OBJS=frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o
    31 SDK_LIB_OBJS= $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(GENOTYPE_LOADER_OBJS) common/virtfile/stdiofile.o
     38SDK_LIB_OBJS= $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(GENOTYPE_LOADER_OBJS) common/virtfile/stdiofile.o
    3239
    3340#### sdk_tests
    3441
    35 GENOMANIPULATION_OBJS= frams/_demos/genomanipulation.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     42GENOMANIPULATION_OBJS= frams/_demos/genomanipulation.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    3643
    37 MULTILINE_F0_OBJS=frams/_demos/multiline_f0_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     44MULTILINE_F0_OBJS=frams/_demos/multiline_f0_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    3845
    3946F0_VARIANTS_OBJS=frams/_demos/f0_variants_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS)
    … …  
    4754GENOCONV_TEST_OBJS= frams/_demos/genoconv_test.o frams/_demos/printconvmap.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS)
    4855
    49 GENO_TEST_OBJS= frams/_demos/geno_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     56GENO_TEST_OBJS= frams/_demos/geno_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    5057
    51 GENOOPER_TEST_OBJS=frams/_demos/genooper_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     58GENOOPER_TEST_OBJS=frams/_demos/genooper_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    5259
    53 GENOOPER_TEST_FTEST_OBJS=frams/_demos/genooper_test_fTest.o common/virtfile/virtfile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS) $(GENMAN_FT)
     60GENOOPER_TEST_FTEST_OBJS=frams/_demos/genooper_test_fTest.o common/virtfile/virtfile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GENMAN_FT)
    5461
    5562NEURO_TEST_OBJS= frams/_demos/neuro_test.o $(STDOUT_LOGGER_OBJS)  \
    5663        frams/neuro/neuroimpl.o frams/neuro/neurofactory.o frams/neuro/impl/neuroimpl-simple.o frams/neuro/impl/neuroimpl-channels.o \
    57         frams/neuro/impl/neuroimpl-fuzzy.o frams/neuro/impl/neuroimpl-fuzzy-f0.o  $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     64        frams/neuro/impl/neuroimpl-fuzzy.o frams/neuro/impl/neuroimpl-fuzzy-f0.o  $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    5865
    59 FULL_PROPS_OBJS= frams/_demos/full_props.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     66FULL_PROPS_OBJS= frams/_demos/full_props.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    6067
    61 SHAPECONVERT_OBJS= frams/_demos/shapeconvert.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     68SHAPECONVERT_OBJS= frams/_demos/shapeconvert.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    6269
    6370SERIAL_TEST_OBJS= frams/_demos/serial_test.o common/virtfile/virtfile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS)
    … …  
    6572PART_SHAPES_OBJS= frams/_demos/part_shapes.o common/virtfile/virtfile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS)
    6673
    67 NEURO_LAYOUT_TEST_OBJS= frams/_demos/neuro_layout_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS) frams/canvas/nn_layout_model.o frams/canvas/nn_simple_layout.o frams/canvas/nn_smart_layout.o
     74NEURO_LAYOUT_TEST_OBJS= frams/_demos/neuro_layout_test.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) frams/canvas/nn_layout_model.o frams/canvas/nn_simple_layout.o frams/canvas/nn_smart_layout.o
    6875
    69 GEOMETRY_INFO_TEST_OBJS=frams/_demos/geometry/info_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GEOMETRY_OBJS) $(GENMAN_SDK_OBJS) $(STDOUT_LOGGER_OBJS)
     76GEOMETRY_INFO_TEST_OBJS=frams/_demos/geometry/info_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(STDOUT_LOGGER_OBJS)
    7077
    71 GEOMETRY_SURFACE_TEST_OBJS=frams/_demos/geometry/surface_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GEOMETRY_OBJS) $(GENMAN_SDK_OBJS) $(STDOUT_LOGGER_OBJS)
     78GEOMETRY_SURFACE_TEST_OBJS=frams/_demos/geometry/surface_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(STDOUT_LOGGER_OBJS)
    7279
    73 GEOMETRY_VOLUME_TEST_OBJS=frams/_demos/geometry/volume_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GEOMETRY_OBJS) $(GENMAN_SDK_OBJS) $(STDOUT_LOGGER_OBJS)
     80GEOMETRY_VOLUME_TEST_OBJS=frams/_demos/geometry/volume_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(STDOUT_LOGGER_OBJS)
    7481
    75 GEOMETRY_APICES_TEST_OBJS=frams/_demos/geometry/apices_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GEOMETRY_OBJS) $(GENMAN_SDK_OBJS) $(STDOUT_LOGGER_OBJS)
     82GEOMETRY_APICES_TEST_OBJS=frams/_demos/geometry/apices_test.o frams/_demos/geometry/geometrytestutils.o frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) $(GEOMETRY_OBJS) $(STDOUT_LOGGER_OBJS)
    7683
    7784SIMIL_TEST_OBJS=frams/_demos/simil_test.o frams/model/similarity/SVD/lapack.o frams/model/similarity/SVD/matrix_tools.o frams/model/similarity/simil_match.o frams/model/similarity/simil_model.o  \
    78      frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS)
     85     frams/_demos/genotypeloader.o frams/_demos/genotypemini.o frams/param/multiparamload.o common/virtfile/stdiofile.o $(STDOUT_LOGGER_OBJS) $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS)
    7986
    8087SIMIL_UNITTESTS_OBJS=frams/_demos/simil_unittests.o frams/model/similarity/simil_match.o
    … …  
    8289PARAMTREE_STDIN_TEST_OBJS=frams/_demos/paramtree_stdin_test.o frams/_demos/paramtree_print.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) frams/param/paramtree.o
    8390
    84 PARAMTREE_PARAMLIST_TEST_OBJS=frams/_demos/paramtree_paramlist_test.o frams/_demos/paramtree_print.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_SDK_OBJS) $(GENMAN_SDK_OBJS) frams/neuro/neuroimpl.o frams/neuro/neurofactory.o frams/neuro/impl/neuroimpl-simple.o frams/neuro/impl/neuroimpl-channels.o frams/neuro/impl/neuroimpl-fuzzy.o frams/neuro/impl/neuroimpl-fuzzy-f0.o $(GENOTYPE_LOADER_OBJS) $(GEOMETRY_OBJS) frams/model/geometry/modelgeoclass.o frams/model/modelobj.o frams/param/paramtree.o
     91PARAMTREE_PARAMLIST_TEST_OBJS=frams/_demos/paramtree_paramlist_test.o frams/_demos/paramtree_print.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) $(GENOCONV_AND_GENMAN_SDK_OBJS) frams/neuro/neuroimpl.o frams/neuro/neurofactory.o frams/neuro/impl/neuroimpl-simple.o frams/neuro/impl/neuroimpl-channels.o frams/neuro/impl/neuroimpl-fuzzy.o frams/neuro/impl/neuroimpl-fuzzy-f0.o $(GENOTYPE_LOADER_OBJS) $(GEOMETRY_OBJS) frams/model/geometry/modelgeoclass.o frams/model/modelobj.o frams/param/paramtree.o
    8592
    8693MUTABLEPARAM_TEST_OBJS=frams/_demos/mutableparam_test.o $(STDOUT_LOGGER_OBJS) common/virtfile/stdiofile.o $(SDK_OBJS) frams/param/mutableparam.o frams/param/mutparamlist.o frams/param/paramtrans.o

  • cpp/frams/genetics/defgenoconv.cpp

    r779 r780  
    4343#include "fn/fn_conv.h"
    4444#endif
     45#ifdef USE_GENCONV_fBH
     46#include "fB/fB_conv.h"
     47#endif
     48#ifdef USE_GENCONV_fH0
     49#include "fH/fH_conv.h"
     50#endif
     51#ifdef USE_GENCONV_fL0
     52#include "fL/fL_conv.h"
     53#endif
    4554
    4655void DefaultGenoConvManager::addDefaultConverters()
    … …  
    8291        addConverter(new GenoConv_fn0);
    8392#endif
     93#ifdef USE_GENCONV_fBH
     94        addConverter(new GenoConv_fBH);
     95#endif
     96#ifdef USE_GENCONV_fH0
     97        addConverter(new GenoConv_fH0);
     98#endif
     99#ifdef USE_GENCONV_fL0
     100        addConverter(new GenoConv_fL0);
     101#endif
    84102
    85103        param.updatetab();

  • cpp/frams/genetics/gen-config-SDK.h

    r748 r780  
    2121#define USE_GENCONV_fF0
    2222#define USE_GENCONV_fn0
     23#define USE_GENCONV_fBH
     24#define USE_GENCONV_fH0
     25#define USE_GENCONV_fL0
    2326
    2427//#define USE_GENMAN_f0
    … …  
    3235#define USE_GENMAN_fT
    3336#define USE_GENMAN_fn
     37#define USE_GENMAN_fB
     38#define USE_GENMAN_fH
     39#define USE_GENMAN_fL

  • cpp/frams/genetics/genman.cpp

    r779 r780  
    5959#ifdef USE_GENMAN_fT
    6060#include "fT/fTest_oper.h"
     61#endif
     62#ifdef USE_GENMAN_fB
     63#include "fB/fB_oper.h"
     64#endif
     65#ifdef USE_GENMAN_fH
     66#include "fH/fH_oper.h"
     67#endif
     68#ifdef USE_GENMAN_fL
     69#include "fL/fL_oper.h"
    6170#endif
    6271
    … …  
    158167#ifdef USE_GENMAN_fT
    159168        oper_fx_list.push_back(new GenoOper_fTest);
     169#endif
     170#ifdef USE_GENMAN_fB
     171        oper_fx_list.push_back(new Geno_fB);
     172#endif
     173#ifdef USE_GENMAN_fH
     174        oper_fx_list.push_back(new Geno_fH);
     175#endif
     176#ifdef USE_GENMAN_fL
     177        oper_fx_list.push_back(new Geno_fL);
    160178#endif
    161179
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