diff --git a/released_plugins/v3d_plugins/5dstackconverter/movieZCswitch.pro b/released_plugins/v3d_plugins/5dstackconverter/movieZCswitch.pro index 10f767bef6..cb846c4999 100644 --- a/released_plugins/v3d_plugins/5dstackconverter/movieZCswitch.pro +++ b/released_plugins/v3d_plugins/5dstackconverter/movieZCswitch.pro @@ -3,6 +3,8 @@ TEMPLATE = lib CONFIG += qt plugin warn_off INCLUDEPATH += ../../../../v3d_external/v3d_main/basic_c_fun INCLUDEPATH += ../../../../v3d_external/v3d_main/common_lib/include +INCLUDEPATH += ../../../../v3d_external/v3d_main/v3d + HEADERS = movieZCswitch.h SOURCES = movieZCswitch.cpp diff --git a/released_plugins/v3d_plugins/Janelia_blend_multiscanstacks/imageblend.pro b/released_plugins/v3d_plugins/Janelia_blend_multiscanstacks/imageblend.pro index 3b9b25fdfc..5528a1cbe6 100644 --- a/released_plugins/v3d_plugins/Janelia_blend_multiscanstacks/imageblend.pro +++ b/released_plugins/v3d_plugins/Janelia_blend_multiscanstacks/imageblend.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS += y_lsminfo.h HEADERS += imageblend.h diff --git a/released_plugins/v3d_plugins/Janelia_clonalselect/clonalselect.pro b/released_plugins/v3d_plugins/Janelia_clonalselect/clonalselect.pro index ec15af8d76..d0a18529a7 100644 --- a/released_plugins/v3d_plugins/Janelia_clonalselect/clonalselect.pro +++ b/released_plugins/v3d_plugins/Janelia_clonalselect/clonalselect.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS += clonalselect_gui.h HEADERS += clonalselect_core.h diff --git a/released_plugins/v3d_plugins/Janelia_ifusion/ifusion.pro b/released_plugins/v3d_plugins/Janelia_ifusion/ifusion.pro index d0ccbfa68c..58b6d3954a 100644 --- a/released_plugins/v3d_plugins/Janelia_ifusion/ifusion.pro +++ b/released_plugins/v3d_plugins/Janelia_ifusion/ifusion.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS += ifusion.h HEADERS += $$V3DMAINDIR/basic_c_fun/v3d_message.h diff --git a/released_plugins/v3d_plugins/Janelia_ireg/ireg.pro b/released_plugins/v3d_plugins/Janelia_ireg/ireg.pro index 729e819d24..d17d4693d6 100644 --- a/released_plugins/v3d_plugins/Janelia_ireg/ireg.pro +++ b/released_plugins/v3d_plugins/Janelia_ireg/ireg.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS += ireg.h HEADERS += y_NiftiImageIO.h diff --git a/released_plugins/v3d_plugins/Janelia_istitch/istitch.pro b/released_plugins/v3d_plugins/Janelia_istitch/istitch.pro index 945fb36235..4c854a570a 100644 --- a/released_plugins/v3d_plugins/Janelia_istitch/istitch.pro +++ b/released_plugins/v3d_plugins/Janelia_istitch/istitch.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS = istitch.h HEADERS += istitch_gui.h diff --git a/released_plugins/v3d_plugins/Janelia_lobeseg/lobeseg.pro b/released_plugins/v3d_plugins/Janelia_lobeseg/lobeseg.pro index 15a494e5b9..c40dbb4c8b 100644 --- a/released_plugins/v3d_plugins/Janelia_lobeseg/lobeseg.pro +++ b/released_plugins/v3d_plugins/Janelia_lobeseg/lobeseg.pro @@ -4,7 +4,9 @@ CONFIG += qt plugin warn_off #CONFIG += x86_64 V3DMAINFOLER = ../../../v3d_main -INCLUDEPATH += $$V3DMAINFOLER/basic_c_fun $$V3DMAINFOLER/common_lib/include +INCLUDEPATH += $$V3DMAINFOLER/basic_c_fun +INCLUDEPATH += $$V3DMAINFOLER/common_lib/include +INCLUDEPATH += $$V3DMAINFOLER/v3d LIBS += -L. -lv3dtiff -L$$V3DMAINFOLER/common_lib/lib HEADERS = lobeseg_plugin.h diff --git a/released_plugins/v3d_plugins/Janelia_refextract/refextract.pro b/released_plugins/v3d_plugins/Janelia_refextract/refextract.pro index 8ed5a0be1a..3f3ae366f7 100644 --- a/released_plugins/v3d_plugins/Janelia_refextract/refextract.pro +++ b/released_plugins/v3d_plugins/Janelia_refextract/refextract.pro @@ -7,6 +7,7 @@ V3DMAINDIR = ../../../v3d_main INCLUDEPATH += $$V3DMAINDIR/basic_c_fun INCLUDEPATH += $$V3DMAINDIR/common_lib/include +INCLUDEPATH += $$V3DMAINDIR/v3d HEADERS = refextract.h diff --git a/released_plugins/v3d_plugins/Janelia_ssd_registration/plugin_PQ_imagereg.pro b/released_plugins/v3d_plugins/Janelia_ssd_registration/plugin_PQ_imagereg.pro index 59dca9c629..d3b10a74db 100644 --- a/released_plugins/v3d_plugins/Janelia_ssd_registration/plugin_PQ_imagereg.pro +++ b/released_plugins/v3d_plugins/Janelia_ssd_registration/plugin_PQ_imagereg.pro @@ -13,6 +13,7 @@ V3DPATH = ../../../v3d_main INCLUDEPATH += $$V3DPATH/basic_c_fun INCLUDEPATH += $$V3DPATH/jba/newmat11 INCLUDEPATH += $$V3DPATH/common_lib/include +INCLUDEPATH += $$V3DPATH/v3d #LIBS += -L$$V3DPATH/common_lib/lib -lv3dtiff LIBS += -L$$V3DPATH/jba/c++ -lv3dnewmat diff --git a/released_plugins/v3d_plugins/NifTi_reader/NifTi_reader.pro b/released_plugins/v3d_plugins/NifTi_reader/NifTi_reader.pro index 1a989bb324..7c4b37be89 100644 --- a/released_plugins/v3d_plugins/NifTi_reader/NifTi_reader.pro +++ b/released_plugins/v3d_plugins/NifTi_reader/NifTi_reader.pro @@ -1,7 +1,9 @@ TEMPLATE = lib CONFIG += qt plugin warn_off -VAA3DPATH = ../../../../v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d INCLUDEPATH += ./include macx{ LIBS += ./lib/mac/libz.a @@ -27,7 +29,7 @@ unix:!macx { HEADERS += NifTi_reader_plugin.h SOURCES += NifTi_reader_plugin.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp TARGET = $$qtLibraryTarget(NifTi_reader) -DESTDIR = $$VAA3DPATH/bin/plugins/data_IO/NIFTI_file_reader +DESTDIR = $$V3DMAINPATH/bin/plugins/data_IO/NIFTI_file_reader diff --git a/released_plugins/v3d_plugins/SWC_Resample_plugin/SWC_Resample.pro b/released_plugins/v3d_plugins/SWC_Resample_plugin/SWC_Resample.pro index 1dfe1dfd97..e199960bb0 100644 --- a/released_plugins/v3d_plugins/SWC_Resample_plugin/SWC_Resample.pro +++ b/released_plugins/v3d_plugins/SWC_Resample_plugin/SWC_Resample.pro @@ -2,17 +2,19 @@ TEMPLATE = lib CONFIG += qt plugin warn_off #CONFIG += x86_64 -VAA3DPATH = ../../../../v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d HEADERS += SWC_Resample_plugin.h HEADERS += ../../../released_plugins/v3d_plugins/resample_swc/resampling.h -HEADERS += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.h -HEADERS += $$VAA3DPATH/v3d_main/neuron_editing/neuron_xforms.h +HEADERS += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.h +HEADERS += $$V3DMAINPATH/v3d_main/neuron_editing/neuron_xforms.h SOURCES += SWC_Resample_plugin.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp -SOURCES += $$VAA3DPATH/v3d_main/neuron_editing/neuron_xforms.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/neuron_editing/neuron_xforms.cpp TARGET = $$qtLibraryTarget(SWC_Resample) -DESTDIR = $$VAA3DPATH/bin/plugins/neuron_utilities/swc_gui_resample/ +DESTDIR = $$V3DMAINPATH/bin/plugins/neuron_utilities/swc_gui_resample/ diff --git a/released_plugins/v3d_plugins/TipDetection/TipDetection.pro b/released_plugins/v3d_plugins/TipDetection/TipDetection.pro index 7350755063..bb9f14afbb 100644 --- a/released_plugins/v3d_plugins/TipDetection/TipDetection.pro +++ b/released_plugins/v3d_plugins/TipDetection/TipDetection.pro @@ -2,14 +2,15 @@ TEMPLATE = lib CONFIG += qt plugin warn_off #CONFIG += x86_64 -VAA3DPATH = F:/newv3dcode/v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun -INCLUDEPATH += $$VAA3DPATH/v3d_main/common_lib/include +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d HEADERS += TipDetection_plugin.h SOURCES += TipDetection_plugin.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/basic_surf_objs.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/basic_surf_objs.cpp TARGET = $$qtLibraryTarget(TipDetection) -DESTDIR = $$VAA3DPATH/bin/plugins/bigneuronhackathon/TipDetection/ +DESTDIR = $$V3DMAINPATH/bin/plugins/bigneuronhackathon/TipDetection/ diff --git a/released_plugins/v3d_plugins/ZMovieMaker/ZMovieMaker.pro b/released_plugins/v3d_plugins/ZMovieMaker/ZMovieMaker.pro index 076224e3d6..8d90250cd5 100644 --- a/released_plugins/v3d_plugins/ZMovieMaker/ZMovieMaker.pro +++ b/released_plugins/v3d_plugins/ZMovieMaker/ZMovieMaker.pro @@ -2,13 +2,14 @@ TEMPLATE = lib CONFIG += qt plugin warn_off #CONFIG += x86_64 -VAA3DPATH = ../../../v3d_main -INCLUDEPATH += $$VAA3DPATH/basic_c_fun +V3DMAINPATH = ../../../v3d_main +INCLUDEPATH += $$V3DMAINPATH/basic_c_fun INCLUDEPATH += $$V3DMAINPATH/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d HEADERS += ZMovieMaker_plugin.h SOURCES += ZMovieMaker_plugin.cpp -SOURCES += $$VAA3DPATH/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/basic_c_fun/v3d_message.cpp TARGET = $$qtLibraryTarget(ZMovieMaker) -DESTDIR = $$VAA3DPATH/../bin/plugins/movies_and_snapshots/ZMovieMaker/ +DESTDIR = $$V3DMAINPATH/../bin/plugins/movies_and_snapshots/ZMovieMaker/ diff --git a/released_plugins/v3d_plugins/ada_threshold/ada_threshold.pro b/released_plugins/v3d_plugins/ada_threshold/ada_threshold.pro index dffcb7f81c..ddca450700 100644 --- a/released_plugins/v3d_plugins/ada_threshold/ada_threshold.pro +++ b/released_plugins/v3d_plugins/ada_threshold/ada_threshold.pro @@ -5,6 +5,7 @@ CONFIG += qt plugin warn_off V3DMAINPATH = ../../../v3d_main INCLUDEPATH += $$V3DMAINPATH/basic_c_fun INCLUDEPATH += $$V3DMAINPATH/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d INCLUDEPATH += main HEADERS += ada_threshold.h diff --git a/released_plugins/v3d_plugins/affine_tps_warp/plugin_warp_affine_tps.pro b/released_plugins/v3d_plugins/affine_tps_warp/plugin_warp_affine_tps.pro index 57042d6829..6e569dc591 100644 --- a/released_plugins/v3d_plugins/affine_tps_warp/plugin_warp_affine_tps.pro +++ b/released_plugins/v3d_plugins/affine_tps_warp/plugin_warp_affine_tps.pro @@ -8,6 +8,7 @@ CONFIG -= app_bundle V3DMAINPATH = ../../../v3d_main INCLUDEPATH += $$V3DMAINPATH/basic_c_fun INCLUDEPATH += $$V3DMAINPATH/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d INCLUDEPATH += $$V3DMAINPATH/jba/newmat11 unix { diff --git a/released_plugins/v3d_plugins/affine_transform_swc/affine_transform_swc.pro b/released_plugins/v3d_plugins/affine_transform_swc/affine_transform_swc.pro index f42c5948ae..6be3955951 100644 --- a/released_plugins/v3d_plugins/affine_transform_swc/affine_transform_swc.pro +++ b/released_plugins/v3d_plugins/affine_transform_swc/affine_transform_swc.pro @@ -1,36 +1,37 @@ TEMPLATE = lib CONFIG += qt plugin warn_off -VAA3DPATH = ../../../../v3d_external V3DMAINPATH = ../../../../v3d_external/v3d_main -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d INCLUDEPATH += $$V3DMAINPATH/jba/newmat11 macx{ - LIBS += -L$$VAA3DPATH/v3d_main/jba/c++ -lv3dnewmat + LIBS += -L$$V3DMAINPATH/jba/c++ -lv3dnewmat # CONFIG += x86_64 } win32{ - LIBS += -L$$VAA3DPATH/v3d_main/common_lib/winlib64 -llibnewmat + LIBS += -L$$V3DMAINPATH/common_lib/winlib64 -llibnewmat } unix:!macx { - LIBS += -L$$VAA3DPATH/v3d_main/jba/c++ -lv3dnewmat + LIBS += -L$$V3DMAINPATH/jba/c++ -lv3dnewmat } HEADERS += affine_transform_swc_plugin.h HEADERS += apply_transform_func.h -HEADERS += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.h +HEADERS += $$V3DMAINPATH/basic_c_fun/v3d_message.h HEADERS += io_affine_transform.h SOURCES += affine_transform_swc_plugin.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/basic_surf_objs.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/basic_c_fun/basic_surf_objs.cpp +SOURCES += $$V3DMAINPATH/basic_c_fun/v3d_message.cpp SOURCES += apply_transform_func.cpp SOURCES += io_affine_transform.cpp TARGET = $$qtLibraryTarget(affine_transform_swc) -DESTDIR = $$VAA3DPATH/bin/plugins/neuron_utilities/affine_transform_swc/ +DESTDIR = $$V3DMAINPATH/bin/plugins/neuron_utilities/affine_transform_swc/ diff --git a/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_RegMST_tracing_plugin/RegMST.pro b/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_RegMST_tracing_plugin/RegMST.pro index 090e2ca071..95b875b875 100755 --- a/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_RegMST_tracing_plugin/RegMST.pro +++ b/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_RegMST_tracing_plugin/RegMST.pro @@ -12,12 +12,14 @@ else{ SOURCES = ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/ITK_include/itkLightProcessObject.cxx } -VAA3DPATH = ../../../../v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d -INCLUDEPATH += $$VAA3DPATH/v3d_main/neuron_editing -INCLUDEPATH += $$VAA3DPATH/v3d_main/worm_straighten_c -INCLUDEPATH += $$VAA3DPATH/v3d_main/cellseg +INCLUDEPATH += $$V3DMAINPATH/v3d_main/neuron_editing +INCLUDEPATH += $$V3DMAINPATH/v3d_main/worm_straighten_c +INCLUDEPATH += $$V3DMAINPATH/v3d_main/cellseg #INCLUDEPATH += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/liblbfgs-1.10/include @@ -30,7 +32,7 @@ INCLUDEPATH += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/IT INCLUDEPATH += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regression INCLUDEPATH += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/sqb_0.1/src/MatrixSQB INCLUDEPATH += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/boost_1_58_0 -INCLUDEPATH += $$VAA3DPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include LIBS += -L$$ITKLIBPATH -litksys-4.5 -lITKCommon-4.5 -lITKStatistics-4.5 -lITKIOImageBase-4.5 -litkdouble-conversion-4.5 LIBS += -L$$ITKLIBPATH -lvnl_algo -lvnl -lv3p_netlib @@ -49,29 +51,29 @@ HEADERS += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regres HEADERS += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regression/sampling.h HEADERS += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regression/regressor.h -HEADERS += $$VAA3DPATH/v3d_main/basic_c_fun/mg_utilities.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/basic_memory.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/stackutil.h\ - $$VAA3DPATH/v3d_main/basic_c_fun/mg_image_lib.h\ - $$VAA3DPATH/v3d_main/basic_c_fun/img_definition.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/volimg_proc_declare.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/volimg_proc.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/color_xyz.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/basic_surf_objs.h \ - $$VAA3DPATH/v3d_main/basic_c_fun/basic_landmark.h \ - $$VAA3DPATH/v3d_main/graph/graph.h \ - $$VAA3DPATH/v3d_main/graph/graph_basic.h \ - $$VAA3DPATH/v3d_main/graph/dijk.h \ - $$VAA3DPATH/v3d_main/worm_straighten_c/bdb_minus.h \ - $$VAA3DPATH/v3d_main/worm_straighten_c/mst_prim_c.h \ - $$VAA3DPATH/v3d_main/worm_straighten_c/bfs.h \ - $$VAA3DPATH/v3d_main/worm_straighten_c/spline_cubic.h \ - $$VAA3DPATH/v3d_main/neuron_editing/apo_xforms.h \ - $$VAA3DPATH/v3d_main/neuron_editing/neuron_xforms.h \ - $$VAA3DPATH/v3d_main/neuron_editing/neuron_sim_scores.h \ - $$VAA3DPATH/v3d_main/neuron_editing/v_neuronswc.h \ - $$VAA3DPATH/v3d_main/cellseg/template_matching_seg.h \ +HEADERS += $$V3DMAINPATH/v3d_main/basic_c_fun/mg_utilities.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/basic_memory.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/stackutil.h\ + $$V3DMAINPATH/v3d_main/basic_c_fun/mg_image_lib.h\ + $$V3DMAINPATH/v3d_main/basic_c_fun/img_definition.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/volimg_proc_declare.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/volimg_proc.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/color_xyz.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/basic_surf_objs.h \ + $$V3DMAINPATH/v3d_main/basic_c_fun/basic_landmark.h \ + $$V3DMAINPATH/v3d_main/graph/graph.h \ + $$V3DMAINPATH/v3d_main/graph/graph_basic.h \ + $$V3DMAINPATH/v3d_main/graph/dijk.h \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/bdb_minus.h \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/mst_prim_c.h \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/bfs.h \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/spline_cubic.h \ + $$V3DMAINPATH/v3d_main/neuron_editing/apo_xforms.h \ + $$V3DMAINPATH/v3d_main/neuron_editing/neuron_xforms.h \ + $$V3DMAINPATH/v3d_main/neuron_editing/neuron_sim_scores.h \ + $$V3DMAINPATH/v3d_main/neuron_editing/v_neuronswc.h \ + $$V3DMAINPATH/v3d_main/cellseg/template_matching_seg.h \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/FL_bwdist.h \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/gd.h \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/tip_detection.h \ @@ -86,20 +88,20 @@ SOURCES += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regres SOURCES += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regression/sampling.cpp SOURCES += ../bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/libs/regression/regressor.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/mg_utilities.cpp \ - $$VAA3DPATH/v3d_main/basic_c_fun/basic_memory.cpp \ - $$VAA3DPATH/v3d_main/basic_c_fun/stackutil.cpp\ - $$VAA3DPATH/v3d_main/basic_c_fun/mg_image_lib.cpp\ - $$VAA3DPATH/v3d_main/graph/dijk.cpp \ - $$VAA3DPATH/v3d_main/worm_straighten_c/bdb_minus.cpp \ - $$VAA3DPATH/v3d_main/worm_straighten_c/mst_prim_c.cpp \ - $$VAA3DPATH/v3d_main/worm_straighten_c/bfs_1root.cpp \ - $$VAA3DPATH/v3d_main/worm_straighten_c/spline_cubic.cpp \ - $$VAA3DPATH/v3d_main/neuron_editing/apo_xforms.cpp \ - $$VAA3DPATH/v3d_main/neuron_editing/neuron_xforms.cpp \ - $$VAA3DPATH/v3d_main/neuron_editing/neuron_sim_scores.cpp \ - $$VAA3DPATH/v3d_main/neuron_editing/v_neuronswc.cpp \ - $$VAA3DPATH/v3d_main/cellseg/template_matching_seg.cpp \ +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/mg_utilities.cpp \ + $$V3DMAINPATH/v3d_main/basic_c_fun/basic_memory.cpp \ + $$V3DMAINPATH/v3d_main/basic_c_fun/stackutil.cpp\ + $$V3DMAINPATH/v3d_main/basic_c_fun/mg_image_lib.cpp\ + $$V3DMAINPATH/v3d_main/graph/dijk.cpp \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/bdb_minus.cpp \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/mst_prim_c.cpp \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/bfs_1root.cpp \ + $$V3DMAINPATH/v3d_main/worm_straighten_c/spline_cubic.cpp \ + $$V3DMAINPATH/v3d_main/neuron_editing/apo_xforms.cpp \ + $$V3DMAINPATH/v3d_main/neuron_editing/neuron_xforms.cpp \ + $$V3DMAINPATH/v3d_main/neuron_editing/neuron_sim_scores.cpp \ + $$V3DMAINPATH/v3d_main/neuron_editing/v_neuronswc.cpp \ + $$V3DMAINPATH/v3d_main/cellseg/template_matching_seg.cpp \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/gd.cpp \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/tip_detection.cpp \ ../../../released_plugins/v3d_plugins/neurontracing_vn2/app1/autoseed.cpp \ @@ -108,8 +110,8 @@ SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/mg_utilities.cpp \ SOURCES += mst_functions/neurontracing_mst_plugin.cpp SOURCES += RegMST_plugin.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/basic_surf_objs.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/basic_surf_objs.cpp QMAKE_CXXFLAGS += -DLIBCONFIGXX_VER_REVISION QMAKE_CXXFLAGS += -fPIC @@ -117,4 +119,4 @@ QMAKE_CXXFLAGS += -fopenmp QMAKE_LFLAGS += -fopenmp TARGET = $$qtLibraryTarget(RegMST) -DESTDIR = $$VAA3DPATH/bin/plugins/neuron_tracing/RegMST/ +DESTDIR = $$V3DMAINPATH/bin/plugins/neuron_tracing/RegMST/ diff --git a/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/RegressionTubularityAC.pro b/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/RegressionTubularityAC.pro index 69a659295d..b56752b7b7 100755 --- a/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/RegressionTubularityAC.pro +++ b/released_plugins/v3d_plugins/bigneuron_AmosSironi_PrzemyslawGlowacki_SQBTree_plugin/RegressionTubularityAC.pro @@ -12,8 +12,10 @@ else{ SOURCES = ./libs/ITK_include/itkLightProcessObject.cxx } -VAA3DPATH = ../../../../v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d #INCLUDEPATH += ./libs/liblbfgs-1.10/include @@ -25,13 +27,13 @@ INCLUDEPATH += ./libs/ITK_include INCLUDEPATH += ./libs/regression INCLUDEPATH += ./libs/sqb_0.1/src/MatrixSQB INCLUDEPATH += ./libs/boost_1_58_0 -INCLUDEPATH += $$VAA3DPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include LIBS += -L$$ITKLIBPATH -litksys-4.5 -lITKCommon-4.5 -lITKStatistics-4.5 -lITKIOImageBase-4.5 -litkdouble-conversion-4.5 LIBS += -L$$ITKLIBPATH -lvnl_algo -lvnl -lv3p_netlib -LIBS += -L$$VAA3DPATH/v3d_main/common_lib/lib -lv3dtiff +LIBS += -L$$V3DMAINPATH/v3d_main/common_lib/lib -lv3dtiff @@ -54,7 +56,7 @@ HEADERS += ./libs/regression/regressor.h HEADERS += RegressionTubularityAC_plugin.h -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp SOURCES += ./libs/regression/sep_conv.cpp SOURCES += ./libs/regression/sampling.cpp SOURCES += ./libs/regression/regressor.cpp @@ -68,4 +70,4 @@ QMAKE_LFLAGS += -fopenmp TARGET = $$qtLibraryTarget(RegressionTubularityAC) -DESTDIR = $$VAA3DPATH/bin/plugins/image_segmentation/RegressionTubularityAC/ +DESTDIR = $$V3DMAINPATH/bin/plugins/image_segmentation/RegressionTubularityAC/ diff --git a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/N3DFix.pro b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/N3DFix.pro index e23d9cde7d..7905fd0cb6 100644 --- a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/N3DFix.pro +++ b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/N3DFix.pro @@ -2,8 +2,10 @@ TEMPLATE = lib CONFIG += qt plugin warn_off #CONFIG += x86_64 -VAA3DPATH = ../../../../v3d_external -INCLUDEPATH += $$VAA3DPATH/v3d_main/basic_c_fun +V3DMAINPATH = ../../../../v3d_external +INCLUDEPATH += $$V3DMAINPATH/v3d_main/basic_c_fun +INCLUDEPATH += $$V3DMAINPATH/v3d_main/common_lib/include +INCLUDEPATH += $$V3DMAINPATH/v3d_main/v3d HEADERS += N3DFix_plugin.h \ Dend_Section.h \ @@ -17,7 +19,7 @@ SOURCES += N3DFix_plugin.cpp \ Load_and_Write_DATA.cpp \ openSWCDialog.cpp \ ../../../../v3d_external/v3d_main/basic_c_fun/basic_surf_objs.cpp -SOURCES += $$VAA3DPATH/v3d_main/basic_c_fun/v3d_message.cpp +SOURCES += $$V3DMAINPATH/v3d_main/basic_c_fun/v3d_message.cpp TARGET = $$qtLibraryTarget(N3DFix) -DESTDIR = $$VAA3DPATH/bin/plugins/neuron_utilities/N3DFix/ +DESTDIR = $$V3DMAINPATH/bin/plugins/neuron_utilities/N3DFix/ diff --git a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/myFuncs.cpp b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/myFuncs.cpp index 5ed21e32db..e32cfe6c49 100644 --- a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/myFuncs.cpp +++ b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/myFuncs.cpp @@ -120,7 +120,7 @@ double RandGen(double A, double B) { A=B; B=temp; } - if (abs(B-A)<1e-6){ + if (fabs(B-A)<1e-6){ return A; }else{ double random = ((double) rand()) / (double) RAND_MAX; @@ -151,14 +151,14 @@ void Calculate_Baseline( std::vector DIAM,std::vector ARC, std:: median_D = MEDIAN(DIAM); for(unsigned i = 0; i < Npoints; i = i + 1) { - r_mad[i] = abs( DIAM[i] - median_D ); + r_mad[i] = fabs( DIAM[i] - median_D ); } mad = MEDIAN(r_mad); // use fitting weights to exclude the outliers if( mad > 1.0e-6 ) { for(unsigned i = 0; i < Npoints; i = i + 1 ) { - r_mad[i] = abs( DIAM[i] - median_D ) / mad; + r_mad[i] = fabs( DIAM[i] - median_D ) / mad; if( r_mad[i] > outlier_cutoff ) { weights[i] = 0.0; } else { @@ -175,13 +175,13 @@ void Calculate_Baseline( std::vector DIAM,std::vector ARC, std:: } median_D = MEDIAN(DIAM_noise); for(unsigned i = 0; i < Npoints; i = i + 1) { - r_mad[i] = abs( DIAM_noise[i] - median_D ); + r_mad[i] = fabs( DIAM_noise[i] - median_D ); } mad = MEDIAN(r_mad); if( mad > 1.0e-6 ) { for(unsigned i = 0; i < Npoints; i = i + 1 ) { - r_mad[i] = abs( DIAM_noise[i] - median_D ) / mad; + r_mad[i] = fabs( DIAM_noise[i] - median_D ) / mad; if( r_mad[i] > outlier_cutoff ) { weights[i] = 0.0; } else { @@ -193,7 +193,7 @@ void Calculate_Baseline( std::vector DIAM,std::vector ARC, std:: double s = STDEV(DIAM); median_D = MEDIAN(DIAM); for(unsigned i = 0; i < Npoints; i = i + 1 ) { - if( abs( DIAM[i] - median_D ) > 2.0 * s ) { + if( fabs( DIAM[i] - median_D ) > 2.0 * s ) { weights[i] = 0.0; } else { weights[i] = 1.0; diff --git a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/remove_artifacts.cpp b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/remove_artifacts.cpp index 171a455e06..b90e08b1e0 100644 --- a/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/remove_artifacts.cpp +++ b/released_plugins/v3d_plugins/bigneuron_ECondeSousa_N3DFix/remove_artifacts.cpp @@ -103,11 +103,11 @@ void N3DFix_v2(std::vector< std::vector > &dend , unsigned de // rnorm rnorm.push_back( DIAM[p] / baseline[p]); // slope - if( abs( ARC[p] - ARC[p-1] ) < 1.0e-6){ - if( abs( DIAM[p] - DIAM[p-1] ) < 1.0e-6){ + if( fabs( ARC[p] - ARC[p-1] ) < 1.0e-6){ + if( fabs( DIAM[p] - DIAM[p-1] ) < 1.0e-6){ slope.push_back(0.0); // ATENTION!!! equal points are not removed! slope is set to zero! }else{ - double sign = ( DIAM[p] - DIAM[p-1] ) / abs( DIAM[p] - DIAM[p-1] ); + double sign = ( DIAM[p] - DIAM[p-1] ) / fabs( DIAM[p] - DIAM[p-1] ); slope.push_back( 2.0 * sign * bump_slope); // ATENTION!!! same (x,y,z) but abrupt change in r! give the slope trigger } }else{// normal case @@ -122,7 +122,7 @@ void N3DFix_v2(std::vector< std::vector > &dend , unsigned de std::vector signal_cor; signal_cor.push_back(0); for(unsigned p =1; p > &dend , unsigned de } double delta_x = ARC[p2]-ARC[p1]; - if (abs(delta_x)>1.0e-6){ + if (fabs(delta_x)>1.0e-6){ // this IS a bump; remove according with the locations of p1 and p2 //choose r0 according to the location of p1 @@ -192,7 +192,7 @@ void N3DFix_v2(std::vector< std::vector > &dend , unsigned de //p2 is a node //force end diam to baseline level m = (baseline[p2]-r0) / delta_x; - if(m > bump_slope || abs(DIAM[p2]/baseline[p2] - 1) > bump_rnorm){ + if(m > bump_slope || fabs(DIAM[p2]/baseline[p2] - 1) > bump_rnorm){ m = (MEDIAN(DIAM)-r0) / delta_x; } } @@ -205,7 +205,7 @@ void N3DFix_v2(std::vector< std::vector > &dend , unsigned de //printf("%g\n",DIAM_new[i]); } - }else{//abs(delta_x)<=1.0e-6 + }else{//fabs(delta_x)<=1.0e-6 for (long i=p1;i<=p2;i=i+1){ DIAM_new[i] = baseline[i]; } @@ -231,7 +231,7 @@ void N3DFix_v2(std::vector< std::vector > &dend , unsigned de }else{ for(unsigned ii=0;ii *)(output.at(0).p))->at(0)); - myfile<<"same:"<