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#
# This file is part of MIA - a toolbox for medical image analysis
# Copyright (c) Leipzig, Madrid 1999-2014 Gert Wollny
#
# MIA 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.
#
# This program 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 this program; if not, see <http://www.gnu.org/licenses/>.
#
#
ADD_CUSTOM_TARGET(manpages)
ADD_CUSTOM_TARGET(XMLDOC)
ADD_CUSTOM_TARGET(mandir COMMAND mkdir -p ${CMAKE_BINARY_DIR}/doc/man)
LINK_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}/../mia/core)
LINK_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}/../mia/2d)
LINK_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}/../mia/3d)
#basic helpers
DEFEXE(filenumberpattern miacore )
DEFEXE(cmeans miacore )
DEFEXE(labelsort miacore )
DEFEXE(wavelettrans miacore )
DEFEXE(myowavelettest miacore )
#2D programs
DEFEXE(2dimagefilter mia2d )
DEFEXE(2dcost mia2d )
DEFEXE(2ddistance mia2d )
DEFEXE(multihist mia2d )
DEFEXE(2dimagestats mia2d )
DEFEXE(2dimagefilterstack mia2d )
DEFEXE(2dimagecreator mia2d )
DEFEXE(2dimagecombiner mia2d )
DEFEXE(raw2image mia2d )
DEFEXE(2ddeform mia2d )
DEFEXE(2dtransform mia2d )
DEFEXE(2dforce mia2d )
DEFEXE(2davgmasked mia2d )
DEFEXE(2dimageregistration mia2d )
DEFEXE(2dimageselect mia2d )
DEFEXE(2dimagecombine-dice mia2d )
DEFEXE(2dfuzzysegment mia2d )
DEFEXE(2dsegment-ahmed mia2d )
DEFEXE(2dsegment-fuzzyw mia2d )
DEFEXE(2dmultiimagevar mia2d )
#DEFEXE(2dmulti-force mia2d )
DEFEXE(2dimagefullstats mia2d )
DEFEXE(2dbinarycombine mia2d )
DEFEXE(2dtransformation-to-strain mia2d)
DEFEXE(2dimageseries-maximum-intensity-projection mia2d)
DEFCHKEXE(2dlerp mia2d )
#Programs related to 2D myocardic perfusion
DEFCHKEXE(2dsegshift mia2dmyocardperf )
DEFEXE(2dsegshiftperslice mia2dmyocardperf )
DEFEXE(2dsegseriesstats mia2dmyocardperf )
DEFEXE(2dseries2dordermedian mia2dmyocardperf )
DEFEXE(2dmyoserial-nonrigid mia2dmyocardperf )
DEFEXE(2dmyoperiodic-nonrigid mia2dmyocardperf )
DEFEXE(2dseriescorr mia2dmyocardperf )
DEFEXE(2dseriesgradvariation mia2dmyocardperf )
DEFEXE(2dseriesgradMAD mia2dmyocardperf )
DEFEXE(2dseriessmoothgradMAD mia2dmyocardperf )
DEFEXE(2dsegmentcropbox mia2dmyocardperf )
DEFEXE(2dseghausdorff mia2dmyocardperf )
DEFEXE(2dserieshausdorff mia2dmyocardperf )
DEFEXE(2dsegcompare mia2dmyocardperf )
DEFEXE(2dgroundtruthreg mia2dmyocardperf )
DEFEXE(2dseries2sets mia2dmyocardperf )
DEFEXE(2dseries-segdistance mia2dmyocardperf )
DEFEXE(2dseries-mincorr mia2dmyocardperf )
DEFEXE(2dseries-sectionmask mia2dmyocardperf )
DEFEXE(2dmyoseries-dice mia2dmyocardperf )
DEFEXE(2dmyoseries-compdice mia2dmyocardperf )
DEFEXE(2dmyocard-segment mia2dmyocardperf )
DEFEXE(2dmyopgt-nonrigid mia2dmyocardperf )
DEFEXE(2dmany2one-nonrigid mia2dmyocardperf )
DEFEXE(2dmyoset-all2one-nonrigid mia2dmyocardperf )
IF(ITPP_FOUND)
DEFEXE(2dmyoica-full mia2dmyocardperf )
DEFEXE(2dmyoicapgt mia2dmyocardperf )
DEFEXE(2dmyomilles mia2dmyocardperf )
DEFEXE(2dmyocard-ica mia2dmyocardperf )
DEFEXE(2dmyocard-icaseries mia2dmyocardperf )
DEFEXE(2dmyoica-nonrigid mia2dmyocardperf )
DEFEXE(2dmyoica-nonrigid-parallel mia2dmyocardperf )
DEFEXE(2dmyoica-nonrigid2 mia2dmyocardperf )
SET(PERF_AND_3D_LIBS mia3d mia2dmyocardperf)
DEFEXE(2dseriestovolume "${PERF_AND_3D_LIBS}")
ENDIF(ITPP_FOUND)
DEFEXE(2dgrayimage-combine-to-rgb mia2d)
DEFEXE(2deval-transformquantity mia2d)
DEFEXE(2dtrackpixelmovement mia2d )
DEFCHKEXE(3dlerp mia3d )
DEFEXE(2dmultiimageto3d mia3d )
DEFEXE(3dimagestats mia3d )
DEFEXE(3dcost mia3d )
DEFEXE(3ddistance mia3d )
DEFEXE(3dimagefilter mia3d )
DEFEXE(3dimagecombine mia3d )
DEFEXE(3dimagecreator mia3d )
DEFEXE(3dimagefilterstack mia3d )
DEFEXE(raw2volume mia3d )
DEFEXE(3dcrispsegment mia3d )
DEFEXE(3ddeform mia3d )
DEFEXE(3dforce mia3d )
DEFEXE(3dfuzzysegment mia3d )
DEFEXE(3dgetslice mia3d )
DEFEXE(3dgetsize mia3d )
DEFEXE(2dto3dimage mia3d )
DEFEXE(2dto3dimageb mia3d )
DEFEXE(3drigidreg mia3d )
DEFEXE(3dnonrigidreg mia3d )
DEFEXE(3dnonrigidreg-alt mia3d )
DEFEXE(2dstackfilter mia3d )
DEFEXE(3dtransform mia3d )
DEFEXE(3dmaskseeded mia3d )
DEFEXE(3dfield2norm mia3d )
DEFEXE(3dimageselect mia3d )
DEFEXE(3dbrainextractT1 mia3d )
DEFEXE(3dbinarycombine mia3d )
DEFEXE(3ddistance-stats mia3d )
DEFEXE(3dimageaddattributes mia3d )
DEFEXE(3dvectorfieldcreate mia3d )
DEFEXE(3dserial-nonrigid mia3d )
DEFEXE(3dmany2one-nonrigid mia3d )
DEFEXE(3dprealign-nonrigid mia3d )
DEFEXE(3dseries-track-intensity mia3d )
DEFEXE(3dtransform2vf mia3d )
DEFEXE(3dtrackpixelmovement mia3d )
DEFEXE(3dvf2transform mia3d )
DEFEXE(3dvfcompare mia3d )
DEFEXE(3deval-transformquantity mia3d)
DEFEXE(3dcost-translatedgrad mia3d)
DEFEXE(3dsegment-ahmed mia3d)
DEFEXE(3dcombine-mr-segmentations mia3d)
DEFEXE(3dlandmarks-transform mia3d)
DEFEXE(3dlandmarks-distances mia3d)
DEFEXE(plugin-help miamesh )
DEFEXE(meshdistance-to-stackmask miamesh )
DEFEXE(meshfilter miamesh )
ADD_EXECUTABLE(mia-test-plugins-as-installed test_plugins_as_installed.cc)
TARGET_LINK_LIBRARIES(mia-test-plugins-as-installed miamesh)
TARGET_LINK_LIBRARIES(mia-test-plugins-as-installed ${BOOST_UNITTEST})
IF(WIN32)
SET_TARGET_PROPERTIES(test-3d-${name} PROPERTIES LINKER_FLAGS "/NODEFAULTLIB:MSVCRT")
ENDIF(WIN32)
IF(ITPP_FOUND)
DEFEXE(3dmotioncompica-nonrigid mia3d )
ENDIF(ITPP_FOUND)
ADD_SUBDIRECTORY(fluid2d )
ADD_SUBDIRECTORY(fluid3d )
ADD_SUBDIRECTORY(isosurface )
ADD_CUSTOM_COMMAND(OUTPUT ${CMAKE_BINARY_DIR}/doc/program.xml
COMMAND ${PYTHON_EXECUTABLE} ARGS ${CMAKE_SOURCE_DIR}/doc/miaxml2sgml.py ${CMAKE_SOURCE_DIR}/doc ${CMAKE_BINARY_DIR}/doc
DEPENDS XMLDOC
)
ADD_CUSTOM_TARGET(process_xml DEPENDS ${CMAKE_BINARY_DIR}/doc/program.xml)
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