CFLAGS = -O2 -ftree-vectorize -fPIC

FFLAGS = -fast -O4

CC =    @CC@ $(CFLAGS)
CXX =   @CXX@ $(CFLAGS)
F77=    @F77@ $(FFLAGS)
LINK=   @LINKER@

BASE = ./src

INSTALLDIR = @prefix@/bin
LIBDIR = @prefix@/lib
INCDIR = @prefix@/include/duchamp

V = @PACKAGE_VERSION@
EXEC = Duchamp-$(V)
EXEC-STUB = Duchamp

AR = ar cq
LIB = libduchamp-$(V).a
LIB_LN = libduchamp.a
RANLIB = ranlib
SHAREDLIB = @SHRLD@
#SHAREDFLAGS = -shared -Wl,-soname,@SHRLIB@
LIBSO = @SHRLIB@
LIBSO_LN = @SHRLN@

INSTALL = @INSTALL@
LN_S = @LN_S@

PGPLOTINC = @PGPLOTINC@
PGPLOTLIB = @PGPLOTLIB@

CFITSIOINC = @CFITSIOINC@
CFITSIOLIB = @CFITSIOLIB@

WCSINC = @WCSINC@
WCSLIB = @WCSLIB@

CINC = -I$(BASE) $(PGPLOTINC) $(WCSINC) $(CFITSIOINC)

LIBS = $(WCSLIB) $(CFITSIOLIB) $(PGPLOTLIB) 

ATROUSDIR = $(BASE)/ATrous
PIXELMAPDIR = $(BASE)/PixelMap
DETECTIONDIR = $(BASE)/Detection
CUBESDIR = $(BASE)/Cubes
FITSIODIR = $(BASE)/FitsIO
PLOTDIR = $(BASE)/Plotting
UTILDIR = $(BASE)/Utils
OUTPUTSDIR = $(BASE)/Outputs
TESTDIR = ./verification

HEADS = $(BASE)/config.h\
	$(BASE)/duchamp.hh\
	$(BASE)/pgheader.hh\
	$(BASE)/param.hh\
	$(BASE)/fitsHeader.hh\
	$(PIXELMAPDIR)/Line.hh\
	$(PIXELMAPDIR)/Voxel.hh\
	$(PIXELMAPDIR)/Scan.hh\
	$(PIXELMAPDIR)/Object2D.hh\
	$(PIXELMAPDIR)/Object3D.hh\
	$(ATROUSDIR)/atrous.hh\
	$(ATROUSDIR)/filter.hh\
	$(ATROUSDIR)/B3SplineFilter.hh\
	$(ATROUSDIR)/TriangleFilter.hh\
	$(ATROUSDIR)/HaarFilter.hh\
	$(ATROUSDIR)/FilterFactory.hh\
	$(DETECTIONDIR)/detection.hh\
	$(DETECTIONDIR)/finders.hh\
	$(DETECTIONDIR)/ObjectGrower.hh\
	$(CUBESDIR)/cubes.hh\
	$(FITSIODIR)/Beam.hh\
	$(FITSIODIR)/DuchampBeam.hh\
	$(FITSIODIR)/ReadExisting.hh\
	$(FITSIODIR)/ReadExistingRecon.hh\
	$(FITSIODIR)/ReadExistingSmooth.hh\
	$(FITSIODIR)/WriteArray.hh\
	$(FITSIODIR)/WriteBaselineArray.hh\
	$(FITSIODIR)/WriteMaskArray.hh\
	$(FITSIODIR)/WriteMomentMapArray.hh\
	$(FITSIODIR)/WriteMomentMaskArray.hh\
	$(FITSIODIR)/WriteReconArray.hh\
	$(FITSIODIR)/WriteSmoothArray.hh\
	$(PLOTDIR)/DuchampPlot.hh\
	$(PLOTDIR)/MultipleDuchampPlot.hh\
	$(PLOTDIR)/ImagePlot.hh\
	$(PLOTDIR)/SpectralPlot.hh\
	$(PLOTDIR)/SimpleSpectralPlot.hh\
	$(PLOTDIR)/CutoutPlot.hh\
	$(UTILDIR)/Hanning.hh\
	$(UTILDIR)/GaussSmooth1D.hh\
	$(UTILDIR)/GaussSmooth2D.hh\
	$(UTILDIR)/Section.hh\
	$(UTILDIR)/Statistics.hh\
	$(UTILDIR)/utils.hh\
	$(UTILDIR)/feedback.hh\
	$(UTILDIR)/mycpgplot.hh\
	$(UTILDIR)/VOField.hh\
	$(UTILDIR)/VOParam.hh\
	$(OUTPUTSDIR)/columns.hh\
	$(OUTPUTSDIR)/CatalogueSpecification.hh\
	$(OUTPUTSDIR)/CatalogueWriter.hh\
	$(OUTPUTSDIR)/FileCatalogueWriter.hh\
	$(OUTPUTSDIR)/ASCIICatalogueWriter.hh\
	$(OUTPUTSDIR)/VOTableCatalogueWriter.hh\
	$(OUTPUTSDIR)/AnnotationWriter.hh\
	$(OUTPUTSDIR)/KarmaAnnotationWriter.hh\
	$(OUTPUTSDIR)/DS9AnnotationWriter.hh\
	$(OUTPUTSDIR)/CasaAnnotationWriter.hh

OBJECTS-NOPG = $(BASE)/mainDuchamp.o \
	$(BASE)/duchamp.o\
	$(BASE)/param.o\
	$(BASE)/fitsHeader.o\
	$(PIXELMAPDIR)/Line.o\
	$(PIXELMAPDIR)/Voxel.o\
	$(PIXELMAPDIR)/Scan.o\
	$(PIXELMAPDIR)/Object2D.o\
	$(PIXELMAPDIR)/Object3D.o\
	$(ATROUSDIR)/filter.o\
	$(ATROUSDIR)/B3SplineFilter.o\
	$(ATROUSDIR)/TriangleFilter.o\
	$(ATROUSDIR)/HaarFilter.o\
	$(ATROUSDIR)/FilterFactory.o\
	$(ATROUSDIR)/atrous_1d_reconstruct.o\
	$(ATROUSDIR)/atrous_2d_reconstruct.o\
	$(ATROUSDIR)/atrous_3d_reconstruct.o\
	$(ATROUSDIR)/baselineSubtract.o\
	$(ATROUSDIR)/ReconSearch.o\
	$(DETECTIONDIR)/detection.o\
	$(DETECTIONDIR)/ObjectGrower.o\
	$(DETECTIONDIR)/areClose.o\
	$(DETECTIONDIR)/lutz_detect.o\
	$(DETECTIONDIR)/mergeIntoList.o\
	$(DETECTIONDIR)/outputDetection.o\
	$(DETECTIONDIR)/sorting.o\
	$(DETECTIONDIR)/spectrumDetect.o\
	$(CUBESDIR)/cubes.o\
	$(CUBESDIR)/cubes_extended.o\
	$(CUBESDIR)/baseline.o\
	$(CUBESDIR)/CubicSearch.o\
	$(CUBESDIR)/detectionIO.o\
	$(CUBESDIR)/existingDetections.o\
	$(CUBESDIR)/getImage.o\
	$(CUBESDIR)/invertCube.o\
	$(CUBESDIR)/Merger.o\
	$(CUBESDIR)/momentMap.o\
	$(CUBESDIR)/smoothCube.o\
	$(CUBESDIR)/spectraUtils.o\
	$(CUBESDIR)/trimImage.o\
	$(FITSIODIR)/Beam.o\
	$(FITSIODIR)/DuchampBeam.o\
	$(FITSIODIR)/ReadExisting.o\
	$(FITSIODIR)/ReadExistingRecon.o\
	$(FITSIODIR)/ReadExistingSmooth.o\
	$(FITSIODIR)/WriteArray.o\
	$(FITSIODIR)/WriteBaselineArray.o\
	$(FITSIODIR)/WriteMaskArray.o\
	$(FITSIODIR)/WriteMomentMapArray.o\
	$(FITSIODIR)/WriteMomentMaskArray.o\
	$(FITSIODIR)/WriteReconArray.o\
	$(FITSIODIR)/WriteSmoothArray.o\
	$(FITSIODIR)/dataIO.o\
	$(FITSIODIR)/headerIO.o\
	$(FITSIODIR)/subsection.o\
	$(FITSIODIR)/wcsIO.o\
	$(UTILDIR)/Section.o\
	$(UTILDIR)/Statistics.o\
	$(UTILDIR)/feedback.o\
	$(UTILDIR)/GaussSmooth1D.o\
	$(UTILDIR)/Hanning.o\
	$(UTILDIR)/VOField.o\
	$(UTILDIR)/VOParam.o\
	$(UTILDIR)/getStats.o\
	$(UTILDIR)/getNormalStats.o\
	$(UTILDIR)/getRobustStats.o\
	$(UTILDIR)/linear_regression.o\
	$(UTILDIR)/medianBaseline.o\
	$(UTILDIR)/position_related.o\
	$(UTILDIR)/sort.o\
	$(UTILDIR)/string_related.o\
	$(UTILDIR)/wcsFunctions.o\
	$(UTILDIR)/zscale.o\
	$(OUTPUTSDIR)/columns.o\
	$(OUTPUTSDIR)/CatalogueSpecification.o\
	$(OUTPUTSDIR)/CatalogueWriter.o\
	$(OUTPUTSDIR)/FileCatalogueWriter.o\
	$(OUTPUTSDIR)/ASCIICatalogueWriter.o\
	$(OUTPUTSDIR)/VOTableCatalogueWriter.o\
	$(OUTPUTSDIR)/AnnotationWriter.o\
	$(OUTPUTSDIR)/KarmaAnnotationWriter.o\
	$(OUTPUTSDIR)/DS9AnnotationWriter.o\
	$(OUTPUTSDIR)/CasaAnnotationWriter.o

ifeq ($(strip $(PGPLOTLIB)),)
  OBJECTS = $(OBJECTS-NOPG)
else
  OBJECTS = $(OBJECTS-NOPG)\
	$(CUBESDIR)/drawBlankEdges.o\
	$(CUBESDIR)/drawMomentCutout.o\
	$(CUBESDIR)/outputSpectra.o\
	$(CUBESDIR)/plotting.o\
	$(DETECTIONDIR)/drawBorders.o\
	$(PLOTDIR)/DuchampPlot.o\
	$(PLOTDIR)/MultipleDuchampPlot.o\
	$(PLOTDIR)/ImagePlot.o\
	$(PLOTDIR)/SpectralPlot.o\
	$(PLOTDIR)/SimpleSpectralPlot.o\
	$(PLOTDIR)/CutoutPlot.o\
	$(UTILDIR)/mycpgplot.o\
	$(UTILDIR)/PlottingUtilities.o\
	$(UTILDIR)/pgplot_related.o
endif

duchamp : $(OBJECTS)
	$(LINK) -o $(EXEC) $(OBJECTS) $(LIBS)

lib     : $(OBJECTS)
	$(AR) $(LIB) $(OBJECTS)
	$(RANLIB) $(LIB)
	$(SHAREDLIB) $(CINC) $(LIBS) -o $(LIBSO) $(OBJECTS)
#	$(CXX) $(SHAREDFLAGS) -o $(LIBSO) $(OBJECTS)

createTestImage : $(TESTDIR)/createTestImage.o $(UTILDIR)/get_random_spectrum.o
	$(CXX) -o createTestImage.x $(TESTDIR)/createTestImage.o $(UTILDIR)/get_random_spectrum.o $(CFITSIOLIB) @LIBS@

install : 
	$(INSTALL) -d -m 2755 $(INSTALLDIR)
	$(INSTALL) -m 755 $(EXEC) $(INSTALLDIR)
	$(RM) $(INSTALLDIR)/$(EXEC-STUB)
	cd $(INSTALLDIR) && $(LN_S) $(EXEC) $(EXEC-STUB)
	-test ! -f $(LIB) || $(INSTALL) -d -m 2755 $(LIBDIR)
	-test ! -f $(LIB) || $(INSTALL) -m 644 $(LIB) $(LIBDIR)
	-test ! -f $(LIB) || ( cd $(LIBDIR) && $(RM) $(LIB_LN) && $(LN_S) $(LIB) $(LIB_LN) )
	-test ! -f $(LIBSO) || ( $(INSTALL) -m 755 $(LIBSO) $(LIBDIR) && \
		if [ "@SHRLN@" != "" ] ; then \
			cd $(LIBDIR) && $(RM) $(LIBSO_LN) && $(LN_S) $(LIBSO) $(LIBSO_LN); \
		fi )
	$(INSTALL) -d -m 2755 $(INCDIR)
	$(INSTALL) -m 644 $(BASE)/*.hh $(INCDIR)
	$(INSTALL) -m 644 $(BASE)/*.h $(INCDIR)
	$(INSTALL) -d -m 2755 $(INCDIR)/Cubes
	$(INSTALL) -m 644 $(CUBESDIR)/*.hh $(INCDIR)/Cubes
	$(INSTALL) -d -m 2755 $(INCDIR)/ATrous
	$(INSTALL) -m 644 $(ATROUSDIR)/*.hh $(INCDIR)/ATrous
	$(INSTALL) -d -m 2755 $(INCDIR)/Detection
	$(INSTALL) -m 644 $(DETECTIONDIR)/*.hh $(INCDIR)/Detection
	$(INSTALL) -d -m 2755 $(INCDIR)/FitsIO
	$(INSTALL) -m 644 $(FITSIODIR)/*.hh $(INCDIR)/FitsIO
	$(INSTALL) -d -m 2755 $(INCDIR)/Plotting
	$(INSTALL) -m 644 $(PLOTDIR)/*.hh $(INCDIR)/Plotting
	$(INSTALL) -d -m 2755 $(INCDIR)/PixelMap
	$(INSTALL) -m 644 $(PIXELMAPDIR)/*.hh $(INCDIR)/PixelMap
	$(INSTALL) -d -m 2755 $(INCDIR)/Outputs
	$(INSTALL) -m 644 $(OUTPUTSDIR)/*.hh $(INCDIR)/Outputs
	$(INSTALL) -d -m 2755 $(INCDIR)/Utils
	$(INSTALL) -m 644 $(UTILDIR)/*.hh $(INCDIR)/Utils
	$(INSTALL) -m 644 $(UTILDIR)/*.tcc $(INCDIR)/Utils

$(OBJECTS) : $(HEADS)

.cc.o:
	$(CXX) -c $< $(CINC) -o $@

.c.o:
	$(CC) -c $< $(CINC) -o $@

clean : 
	rm -f $(BASE)/*.o $(ATROUSDIR)/*.o $(CUBESDIR)/*.o $(FITSIODIR)/*.o $(DETECTIONDIR)/*.o $(UTILDIR)/*.o $(PIXELMAPDIR)/*.o $(PLOTDIR)/*.o $(LIB) $(LIBSO)

cleanest: clean
	rm -rf Makefile config.log config.status src/config.h $(EXEC)