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Makefile
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# LayNii makefile
CC = c++
CFLAGS = -std=c++11 -DHAVE_ZLIB
LFLAGS = -lm -lz
# CFLAGS = -std=c++11 -pedantic -DHAVE_ZLIB -lm -lz
# =============================================================================
LIBRARIES = dep/nifti2_io.cpp \
dep/znzlib.cpp \
dep/laynii_lib.cpp \
-I./dep \
HIGH_PRIORITY = LN_BOCO \
LN_MP2RAGE_DNOISE \
LN2_LAYER_SMOOTH \
LN_LAYER_SMOOTH \
LOW_PRIORITY = LN_3DCOLUMNS \
LN_COLUMNAR_DIST \
LN_CORREL2FILES \
LN_DIRECT_SMOOTH \
LN_GRADSMOOTH \
LN_ZOOM \
LN_FLOAT_ME \
LN_SHORT_ME \
LN_EXTREMETR \
LN_GFACTOR \
LN_GROW_LAYERS \
LN_IMAGIRO \
LN_INTPRO \
LN_LEAKY_LAYERS \
LN_NOISEME \
LN_RAGRUG \
LN_SKEW \
LN_TEMPSMOOTH \
LN_TRIAL \
LN_PHYSIO_PARS \
LN_INT_ME \
LN_LOITUMA \
LN_NOISE_KERNEL \
LN_INFO \
LN_CONLAY \
LN2_DIRECTIONALITY_BIN \
LN2_PHASE_JOLT \
LAYNII2 = LN2_LAYERS \
LN2_COLUMNS \
LN2_CONNECTED_CLUSTERS \
LN2_MULTILATERATE \
LN2_PATCH_FLATTEN \
LN2_PATCH_UNFLATTEN \
LN2_PATCH_FLATTEN_2D \
LN2_CHOLMO \
LN2_PROFILE \
LN2_LAYERDIMENSION \
LN2_MASK \
LN2_BORDERIZE \
LN2_GEODISTANCE \
LN2_IFPOINTS \
LN2_DEVEIN \
LN2_RIMIFY \
LN2_VORONOI \
LN2_ZERO_CROSSING \
LN2_UVD_FILTER \
LN2_HEXBIN \
LN2_NEIGHBORS \
LN2_RIM_POLISH \
LN2_RIM_BORDERIZE \
LN2_SENSITIVITY \
LN2_SPECIFICITY \
DERIVATIVES = LN2_GRADIENTS \
LN2_GRAMAG \
LN2_LAPLACIAN \
LN2_PHASE_GRADIENTS \
LN2_PHASE_LAPLACIAN \
LN2_PHASE_JOLT \
LAYNII = $(LAYNII2) $(HIGH_PRIORITY) $(LOW_PRIORITY) $(DERIVATIVES)
# =============================================================================
all : $(LAYNII)
.PHONY: all $(LAYNII2) $(HIGH_PRIORITY) $(LOW_PRIORITY)
# =============================================================================
# LAYNII programs
LN2_LAYERS:
$(CC) $(CFLAGS) -o LN2_LAYERS src/LN2_LAYERS.cpp $(LIBRARIES) $(LFLAGS)
LN2_LLOYD:
$(CC) $(CFLAGS) -o obj/LN2_LLOYD.o src/LN2_LLOYD.cpp $(LIBRARIES) $(LFLAGS)
LN_BOCO:
$(CC) $(CFLAGS) -o LN_BOCO src/LN_BOCO.cpp $(LIBRARIES) $(LFLAGS)
LN_MP2RAGE_DNOISE:
$(CC) $(CFLAGS) -o LN_MP2RAGE_DNOISE src/LN_MP2RAGE_DNOISE.cpp $(LIBRARIES) $(LFLAGS)
LN_LAYER_SMOOTH:
$(CC) $(CFLAGS) -o LN_LAYER_SMOOTH src/LN_LAYER_SMOOTH.cpp $(LIBRARIES) $(LFLAGS)
LN2_LAYER_SMOOTH:
$(CC) $(CFLAGS) -o LN2_LAYER_SMOOTH src/LN2_LAYER_SMOOTH.cpp $(LIBRARIES) $(LFLAGS)
LN_CORREL2FILES:
$(CC) $(CFLAGS) -o LN_CORREL2FILES src/LN_CORREL2FILES.cpp $(LIBRARIES) $(LFLAGS)
LN_DIRECT_SMOOTH:
$(CC) $(CFLAGS) -o LN_DIRECT_SMOOTH src/LN_DIRECT_SMOOTH.cpp $(LIBRARIES) $(LFLAGS)
LN_GRADSMOOTH:
$(CC) $(CFLAGS) -o LN_GRADSMOOTH src/LN_GRADSMOOTH.cpp $(LIBRARIES) $(LFLAGS)
LN_ZOOM:
$(CC) $(CFLAGS) -o LN_ZOOM src/LN_ZOOM.cpp $(LIBRARIES) $(LFLAGS)
LN_FLOAT_ME:
$(CC) $(CFLAGS) -o LN_FLOAT_ME src/LN_FLOAT_ME.cpp $(LIBRARIES) $(LFLAGS)
LN_SHORT_ME:
$(CC) $(CFLAGS) -o LN_SHORT_ME src/LN_SHORT_ME.cpp $(LIBRARIES) $(LFLAGS)
LN_INT_ME:
$(CC) $(CFLAGS) -o LN_INT_ME src/LN_INT_ME.cpp $(LIBRARIES) $(LFLAGS)
LN_3DCOLUMNS:
$(CC) $(CFLAGS) -o LN_3DCOLUMNS src/LN_3DCOLUMNS.cpp $(LIBRARIES) $(LFLAGS)
LN_COLUMNAR_DIST:
$(CC) $(CFLAGS) -o LN_COLUMNAR_DIST src/LN_COLUMNAR_DIST.cpp $(LIBRARIES) $(LFLAGS)
LN_EXTREMETR:
$(CC) $(CFLAGS) -o LN_EXTREMETR src/LN_EXTREMETR.cpp $(LIBRARIES) $(LFLAGS)
LN_GFACTOR:
$(CC) $(CFLAGS) -o LN_GFACTOR src/LN_GFACTOR.cpp $(LIBRARIES) $(LFLAGS)
LN_GROW_LAYERS:
$(CC) $(CFLAGS) -o LN_GROW_LAYERS src/LN_GROW_LAYERS.cpp $(LIBRARIES) $(LFLAGS)
LN_IMAGIRO:
$(CC) $(CFLAGS) -o LN_IMAGIRO src/LN_IMAGIRO.cpp $(LIBRARIES) $(LFLAGS)
LN_INTPRO:
$(CC) $(CFLAGS) -o LN_INTPRO src/LN_INTPRO.cpp $(LIBRARIES) $(LFLAGS)
LN_LEAKY_LAYERS:
$(CC) $(CFLAGS) -o LN_LEAKY_LAYERS src/LN_LEAKY_LAYERS.cpp $(LIBRARIES) $(LFLAGS)
LN_NOISEME:
$(CC) $(CFLAGS) -o LN_NOISEME src/LN_NOISEME.cpp $(LIBRARIES) $(LFLAGS)
LN_RAGRUG:
$(CC) $(CFLAGS) -o LN_RAGRUG src/LN_RAGRUG.cpp $(LIBRARIES) $(LFLAGS)
LN_SKEW:
$(CC) $(CFLAGS) -o LN_SKEW src/LN_SKEW.cpp $(LIBRARIES) $(LFLAGS)
LN_TEMPSMOOTH:
$(CC) $(CFLAGS) -o LN_TEMPSMOOTH src/LN_TEMPSMOOTH.cpp $(LIBRARIES) $(LFLAGS)
LN_TRIAL:
$(CC) $(CFLAGS) -o LN_TRIAL src/LN_TRIAL.cpp $(LIBRARIES) $(LFLAGS)
LN_LOITUMA:
$(CC) $(CFLAGS) -o LN_LOITUMA src/LN_LOITUMA.cpp $(LIBRARIES) $(LFLAGS)
LN_NOISE_KERNEL:
$(CC) $(CFLAGS) -o LN_NOISE_KERNEL src/LN_NOISE_KERNEL.cpp $(LIBRARIES) $(LFLAGS)
LN2_DIRECTIONALITY_BIN:
$(CC) $(CFLAGS) -o LN2_DIRECTIONALITY_BIN src/LN2_DIRECTIONALITY_BIN.cpp $(LIBRARIES) $(LFLAGS)
LN2_DEVEIN:
$(CC) $(CFLAGS) -o LN2_DEVEIN src/LN2_DEVEIN.cpp $(LIBRARIES) $(LFLAGS)
LN_PHYSIO_PARS:
$(CC) $(CFLAGS) -o LN_PHYSIO_PARS src/LN_PHYSIO_PARS.cpp $(LIBRARIES) $(LFLAGS)
LN2_RIMIFY:
$(CC) $(CFLAGS) -o LN2_RIMIFY src/LN2_RIMIFY.cpp $(LIBRARIES) $(LFLAGS)
LN_INFO:
$(CC) $(CFLAGS) -o LN_INFO src/LN_INFO.cpp $(LIBRARIES) $(LFLAGS)
LN_CONLAY:
$(CC) $(CFLAGS) -o LN_CONLAY src/LN_CONLAY.cpp $(LIBRARIES) $(LFLAGS)
LN2_COLUMNS:
$(CC) $(CFLAGS) -o LN2_COLUMNS src/LN2_COLUMNS.cpp $(LIBRARIES) $(LFLAGS)
LN2_CONNECTED_CLUSTERS:
$(CC) $(CFLAGS) -o LN2_CONNECTED_CLUSTERS src/LN2_CONNECTED_CLUSTERS.cpp $(LIBRARIES) $(LFLAGS)
LN2_MULTILATERATE:
$(CC) $(CFLAGS) -o LN2_MULTILATERATE src/LN2_MULTILATERATE.cpp $(LIBRARIES) $(LFLAGS)
LN2_PATCH_FLATTEN:
$(CC) $(CFLAGS) -o LN2_PATCH_FLATTEN src/LN2_PATCH_FLATTEN.cpp $(LIBRARIES) $(LFLAGS)
LN2_PATCH_FLATTEN_2D:
$(CC) $(CFLAGS) -o LN2_PATCH_FLATTEN_2D src/LN2_PATCH_FLATTEN_2D.cpp $(LIBRARIES) $(LFLAGS)
LN2_PATCH_UNFLATTEN:
$(CC) $(CFLAGS) -o LN2_PATCH_UNFLATTEN src/LN2_PATCH_UNFLATTEN.cpp $(LIBRARIES) $(LFLAGS)
LN2_CHOLMO:
$(CC) $(CFLAGS) -o LN2_CHOLMO src/LN2_CHOLMO.cpp $(LIBRARIES) $(LFLAGS)
LN2_PROFILE:
$(CC) $(CFLAGS) -o LN2_PROFILE src/LN2_PROFILE.cpp $(LIBRARIES) $(LFLAGS)
LN2_LAYERDIMENSION:
$(CC) $(CFLAGS) -o LN2_LAYERDIMENSION src/LN2_LAYERDIMENSION.cpp $(LIBRARIES) $(LFLAGS)
LN2_MASK:
$(CC) $(CFLAGS) -o LN2_MASK src/LN2_MASK.cpp $(LIBRARIES) $(LFLAGS)
LN2_BORDERIZE:
$(CC) $(CFLAGS) -o LN2_BORDERIZE src/LN2_BORDERIZE.cpp $(LIBRARIES) $(LFLAGS)
LN2_GEODISTANCE:
$(CC) $(CFLAGS) -o LN2_GEODISTANCE src/LN2_GEODISTANCE.cpp $(LIBRARIES) $(LFLAGS)
LN2_IFPOINTS:
$(CC) $(CFLAGS) -o LN2_IFPOINTS src/LN2_IFPOINTS.cpp $(LIBRARIES) $(LFLAGS)
LN2_VORONOI:
$(CC) $(CFLAGS) -o LN2_VORONOI src/LN2_VORONOI.cpp $(LIBRARIES) $(LFLAGS)
LN2_ZERO_CROSSING:
$(CC) $(CFLAGS) -o LN2_ZERO_CROSSING src/LN2_ZERO_CROSSING.cpp $(LIBRARIES) $(LFLAGS)
LN2_HEXBIN:
$(CC) $(CFLAGS) -o LN2_HEXBIN src/LN2_HEXBIN.cpp $(LIBRARIES) $(LFLAGS)
LN2_UVD_FILTER:
$(CC) $(CFLAGS) -o LN2_UVD_FILTER src/LN2_UVD_FILTER.cpp $(LIBRARIES) $(LFLAGS)
LN2_RIM_POLISH:
$(CC) $(CFLAGS) -o LN2_RIM_POLISH src/LN2_RIM_POLISH.cpp $(LIBRARIES) $(LFLAGS)
LN2_RIM_BORDERIZE:
$(CC) $(CFLAGS) -o LN2_RIM_BORDERIZE src/LN2_RIM_BORDERIZE.cpp $(LIBRARIES) $(LFLAGS)
LN2_GRADIENTS:
$(CC) $(CFLAGS) -o LN2_GRADIENTS src/LN2_GRADIENTS.cpp $(LIBRARIES) $(LFLAGS)
LN2_GRAMAG:
$(CC) $(CFLAGS) -o LN2_GRAMAG src/LN2_GRAMAG.cpp $(LIBRARIES) $(LFLAGS)
LN2_LAPLACIAN:
$(CC) $(CFLAGS) -o LN2_LAPLACIAN src/LN2_LAPLACIAN.cpp $(LIBRARIES) $(LFLAGS)
LN2_PHASE_GRADIENTS:
$(CC) $(CFLAGS) -o LN2_PHASE_GRADIENTS src/LN2_PHASE_GRADIENTS.cpp $(LIBRARIES) $(LFLAGS)
LN2_PHASE_LAPLACIAN:
$(CC) $(CFLAGS) -o LN2_PHASE_LAPLACIAN src/LN2_PHASE_LAPLACIAN.cpp $(LIBRARIES) $(LFLAGS)
LN2_PHASE_JOLT:
$(CC) $(CFLAGS) -o LN2_PHASE_JOLT src/LN2_PHASE_JOLT.cpp $(LIBRARIES) $(LFLAGS)
LN2_SENSITIVITY:
$(CC) $(CFLAGS) -o LN2_SENSITIVITY src/LN2_SENSITIVITY.cpp $(LIBRARIES) $(LFLAGS)
LN2_SPECIFICITY:
$(CC) $(CFLAGS) -o LN2_SPECIFICITY src/LN2_SPECIFICITY.cpp $(LIBRARIES) $(LFLAGS)
# =============================================================================
# Work in progress programs
LN2_UVD_LSTSQR:
$(CC) $(CFLAGS) -o LN2_UVD_LSTSQR src/LN2_UVD_LSTSQR.cpp $(LIBRARIES) $(LFLAGS)
LN2_PEAK_DETECT:
$(CC) $(CFLAGS) -o LN2_PEAK_DETECT src/LN2_PEAK_DETECT.cpp $(LIBRARIES) $(LFLAGS)
LN2_NEIGHBORS:
$(CC) $(CFLAGS) -o LN2_NEIGHBORS src/LN2_NEIGHBORS.cpp $(LIBRARIES) $(LFLAGS)
LN2_WINDOWED_COUNTER_2D:
$(CC) $(CFLAGS) -o LN2_WINDOWED_COUNTER_2D src/LN2_WINDOWED_COUNTER_2D.cpp $(LIBRARIES) $(LFLAGS)
LN2_SKELETONIZE:
$(CC) $(CFLAGS) -o LN2_SKELETONIZE src/LN2_SKELETONIZE.cpp $(LIBRARIES) $(LFLAGS)
LN2_REGRESS_OUT:
$(CC) $(CFLAGS) -o LN2_REGRESS_OUT src/LN2_REGRESS_OUT.cpp $(LIBRARIES) $(LFLAGS)
LN3_LAYERS:
$(CC) $(CFLAGS) -o LN3_LAYERS src/LN3_LAYERS.cpp $(LIBRARIES) $(LFLAGS)
# =============================================================================
clean:
$(RM) obj/*.o $(LAYNII)
tests:
cd test_data && bash ./tests.sh
# =============================================================================
# Maintenance
# =============================================================================
bump_version:
VERSION=`cat dep/laynii_lib.cpp | grep LayNii | cut -c 21- | rev | cut -c 20- | rev` && \
echo "\nbumping to version: $$VERSION \n" && \
sed -i "s/^version:.*/version: $$VERSION/g" CITATION.cff
make Dockerfile
# =============================================================================
# Docker related content
# =============================================================================
.PHONY: Dockerfile docker_build
Dockerfile:
VERSION=`cat CITATION.cff | grep ^version | cut -c 10-` && \
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base debian:stretch-slim \
--label version=$$VERSION \
--pkg-manager apt \
--install "build-essential libz-dev" \
--run "mkdir /input /output" \
--run "chmod -R 777 /output" \
--user laynii \
--copy dep /home/laynii/dep \
--copy src /home/laynii/src \
--copy Makefile /home/laynii/ \
--workdir /home/laynii/ \
--run "make all" \
--add-to-entrypoint 'PATH=/home/laynii/:$$PATH' > Dockerfile
docker_build:
VERSION=`cat CITATION.cff | grep ^version | cut -c 10-` && \
docker build . -t laynii:$$VERSION -t laynii:latest