# Pipeline for Target lamp

GAIN := $(shell python -c 'import FITS;f=FITS.FITS("flatred.fits");print f["newgain"];f.close()')
all: stage-overscan stage-flatten stage-ydist-copy stage-orders-copy stage-xdist stage-xdist-copy stage-wdist stage-wdist-copy

stage-overscan:
# Overscan Subtraction, Trimming, and Image Reorientation.
	echo Stage:  Overscan Subtraction, Trimming, and Image Reorientation.
	mikebias -c 3 /data1/mifune/kelson/MIKE/sept06/r0050.fits lampred_lamp0050.fits -linebias
	touch stage-overscan

stage-flatten: stage-overscan
# Flattening.
	echo Stage:  Flattening.
	flat2d flatred.fits lampred_lamp0050.fits
	touch stage-flatten

stage-ydist-copy: stage-flatten
# Copying the Y Distortion.
	echo Stage:  Copying the Y Distortion.
	cp ../slitred.fits slitred.fits
	maprect -ydist slitred.fits
	copyrect -ydist slitred.fits lampred_lamp0050f.fits
	touch stage-ydist-copy

stage-orders-copy: stage-ydist-copy
# Copy the Order Edges.
	echo Stage:  Copy the Order Edges.
	copyslit -fwhm 10.000000 -ydist -fft slitred.fits lampred_lamp0050f.fits
	touch stage-orders-copy

stage-xdist: stage-orders-copy
# Get X Distortion.
	echo Stage:  Get X Distortion.
	efits lampred_lamp0050f.fits 'i1-VTKMedian(i1,1,51,numret=1)' lampred_lamp0050fb.fits
	efits lampred_lamp0050fb.fits 'i1-VTKMedian(i1,11,3,numret=1)' lampred_lamp0050fb.fits
	efits lampred_lamp0050fb.fits '1.49*median(abs(i1))' lampred_lamp0050fb_scat.fits
	efits -r lampred_lamp0050fb.fits lampred_lamp0050fb_scat.fits 'bl,bs=bwt(i2);bw=less(i2,bl+100*bs)*ones(i1.shape,Float32);smo=divz(VTKGauss(i1*bw,sigmax=1,sigmay=0,numret=1),VTKGauss(1.*bw,sigmax=1,sigmay=0,numret=1));result=where(bw,i1,smo)' lampred_lamp0050fb.fits
	efits lampred_lamp0050fb.fits 'i1*between(i1,-5*1.49*median(transpose(abs(i1)))[::,NewAxis],65e3)' lampred_lamp0050fb.fits
	getrect -xdist -ydist lampred_lamp0050fb.fits -nx 1 -dy 3 -x 0 -nsub2 1 -y 1 -b 2 -normwt 100.000000 niter 1
	globalrect lampred_lamp0050fb.fits -maxo 2 -go -s 11.000000 -d lampred_lamp0050fbglob.ps/vcps
	maprect -xdist lampred_lamp0050fb.fits
	touch stage-xdist

stage-xdist-copy: stage-xdist
# Copying X Distortion.
	echo Stage:  Copying X Distortion.
	copyrect -xdist lampred_lamp0050fb.fits lampred_lamp0050f.fits
	touch stage-xdist-copy

stage-wdist: stage-xdist-copy
# Do the Wavelength Calibration.
	echo Stage:  Do the Wavelength Calibration.
	mikeMatchOrders lampred_lamp0050fb.fits

	mikeFindLines lampred_lamp0050fbspecs.fits -fwhm 2.500000 -th 10.000000

	mikeMatchLamps lampred_lamp0050fbspecs.fits -x 5 -o 4
	touch stage-wdist

stage-wdist-copy: stage-wdist
	copyecords lampred_lamp0050fbspecs.fits lampred_lamp0050f.fits
	copyecords lampred_lamp0050fbspecs.fits lampred_lamp0050fb.fits


	copyrect -wdist lampred_lamp0050fbspecs.fits lampred_lamp0050f.fits
	copyrect -wdist lampred_lamp0050fbspecs.fits lampred_lamp0050f.fits

	copyrect -edist lampred_lamp0050fbspecs.fits lampred_lamp0050f.fits
	copyrect -edist lampred_lamp0050fbspecs.fits lampred_lamp0050f.fits
	touch stage-wdist-copy

clean:
	rm -f flatred_flat0001.fits flatred_slit0134.fits flatred_flat0002.fits flatred_flat0003.fits flatred_flat0004.fits flatred_flat0005.fits flatred_flat0006.fits flatred_flat0007.fits flatred_flat0008.fits flatred_flat0009.fits flatred_flat0010.fits flatred_flat0011.fits flatred_flat0012.fits flatred_flat0013.fits flatred_flat0014.fits flatred_flat0015.fits flatred_flat0016.fits flatred_flat0017.fits flatred_flat0018.fits flatred_flat0019.fits flatred_flat0020.fits flatred_flat0021.fits flatred_flat0022.fits flatred_flat0023.fits flatred_flat0024.fits flatred_flat0025.fits flatred_flat0026.fits flatred_flat0027.fits flatred_flat0028.fits flatred_flat0029.fits flatred_flat0030.fits flatred_flat0031.fits flatred_flat0032.fits flatred_flat0033.fits flatred_flat0034.fits flatred_flat0035.fits flatred_flat0036.fits flatred_flat0037.fits flatred_flat0038.fits flatred_flat0039.fits flatred_flat0040.fits flatred_flat0041.fits flatred_flat0042.fits flatred_flat0043.fits flatred_flat0044.fits flatred_flat0045.fits flatred_flat0046.fits flatred_flat0087.fits flatred_flat0088.fits flatred_flat0135.fits flatred_flat0136.fits flatred_flat0137.fits flatred_flat0138.fits flatred_flat0139.fits flatred_flat0140.fits flatred_flat0141.fits flatred_flat0142.fits flatred_flat0143.fits flatred_flat0144.fits flatred_flat0145.fits flatred_flat0146.fits flatred_flat0147.fits flatred_flat0148.fits flatred_flat0149.fits flatred_flat0150.fits flatred_flat0151.fits flatred_flat0152.fits flatred_flat0153.fits flatred_flat0154.fits flatred_flat0155.fits flatred_flat0001flt.fits flatred_flat0002flt.fits flatred_flat0003flt.fits flatred_flat0004flt.fits flatred_flat0005flt.fits flatred_flat0006flt.fits flatred_flat0007flt.fits flatred_flat0008flt.fits flatred_flat0009flt.fits flatred_flat0010flt.fits flatred_flat0011flt.fits flatred_flat0012flt.fits flatred_flat0013flt.fits flatred_flat0014flt.fits flatred_flat0015flt.fits flatred_flat0016flt.fits flatred_flat0017flt.fits flatred_flat0018flt.fits flatred_flat0019flt.fits flatred_flat0020flt.fits flatred_flat0021flt.fits flatred_flat0022flt.fits flatred_flat0023flt.fits flatred_flat0024flt.fits flatred_flat0025flt.fits flatred_flat0026flt.fits flatred_flat0027flt.fits flatred_flat0028flt.fits flatred_flat0029flt.fits flatred_flat0030flt.fits flatred_flat0031flt.fits flatred_flat0032flt.fits flatred_flat0033flt.fits flatred_flat0034flt.fits flatred_flat0035flt.fits flatred_flat0036flt.fits flatred_flat0037flt.fits flatred_flat0038flt.fits flatred_flat0039flt.fits flatred_flat0040flt.fits flatred_flat0041flt.fits flatred_flat0042flt.fits flatred_flat0043flt.fits flatred_flat0044flt.fits flatred_flat0045flt.fits flatred_flat0046flt.fits flatred_flat0087flt.fits flatred_flat0088flt.fits flatred_flat0135flt.fits flatred_flat0136flt.fits flatred_flat0137flt.fits flatred_flat0138flt.fits flatred_flat0139flt.fits flatred_flat0140flt.fits flatred_flat0141flt.fits flatred_flat0142flt.fits flatred_flat0143flt.fits flatred_flat0144flt.fits flatred_flat0145flt.fits flatred_flat0146flt.fits flatred_flat0147flt.fits flatred_flat0148flt.fits flatred_flat0149flt.fits flatred_flat0150flt.fits flatred_flat0151flt.fits flatred_flat0152flt.fits flatred_flat0153flt.fits flatred_flat0154flt.fits flatred_flat0155flt.fits slitred_slit0134.fits slitred_slit0156.fits slitred_slit0157.fits slitred_slit0158.fits slitred_slit0159.fits slitred_slit0160.fits slitred_slit0161.fits slitred_slit0162.fits slitred_slit0163.fits slitred_slit0164.fits slitred_slit0165.fits slitred_slit0166.fits slitred_slit0167.fits slitred_slit0168.fits slitred_slit0169.fits slitred_slit0170.fits slitred_slit0171.fits slitred_slit0172.fits slitred_slit0173.fits slitred_slit0174.fits slitred_slit0175.fits slitred_slit0176.fits medianred.fits medianredff.fits lampred_lamp0050.fits lampred_lamp0050f.fits

veryclean:
	rm -f stage-overscan stage-flatten stage-ydist-copy stage-orders-copy stage-xdist stage-xdist-copy stage-wdist stage-wdist-copy