def transform_ap_file(stripfile, wave_step=False, outputfile=None): #2014-01-13 cksim
'''
Apply linear interpolation to the strip with a regular wavelength
- INPUTS :
1. stripfile (FITS)
2. wave_step (to be extracted with this wavelength step for a pixel)
3. outputfile (FITS filename)
- OUTPUTS:
1. tranformed 2D strip data with header
'''
astrip, ahdr = ip.readfits(stripfile)
fpath, fname = ip.split_path(stripfile)
if outputfile == None: outputfile = fpath+fname+'.tr'
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
ny, nx = astrip.shape
yy, xx = np.indices(astrip.shape)
if 'WV-DIM' in ahdr.keys():
xdim, ydim = np.array(ahdr.get('WV-DIM').split(','), dtype=np.int)
wl_coeff = np.zeros([xdim*ydim])
for i in range(xdim):
tmp = ahdr.get('WV-X%03d' % (i,))
wl_coeff[(i*ydim):(i*ydim+ydim)] = np.array(tmp.split(','), dtype=np.double)
awave = ip.polyval2d(xx, yy, wl_coeff, deg=[xdim-1, ydim-1])
else:
print 'No wavelength data in FITS header'
return None, None
if wave_step == False: wave_step = ( (np.max(awave) - np.min(awave)) ) / (nx-1) #2013-01-14 cksim
#--new version--
tstrip, xwave = transform_ap(astrip, awave, wave_step=wave_step)
wv1, wv2 = np.min(xwave), np.max(xwave)
'''old version
wv1, wv2 = (np.min(awave), np.max(awave))
xwave = np.arange(wv1, wv2, wave_step)
nwave = len(xwave)
#print nx, ny, nwave, np.min(awave), np.max(awave)
tstrip = np.zeros([ny,nwave])
for i in range(ny):
row = astrip[i,:]
wv = awave[i,:]
xrow = np.interp(xwave, wv, row)
tstrip[i,:] = xrow
'''
thdr = ahdr.copy()
thdr.update('TRN-TIME', time.strftime('%Y-%m-%d %H:%M:%S'))
# WCS header ========================================
thdr.update('WAT0_001', 'system=world')
thdr.update('WAT1_001', 'wtype=linear label=Wavelength units=microns units_display=microns')
thdr.update('WAT2_001', 'wtype=linear')
thdr.update('WCSDIM', 2)
thdr.update('DISPAXIS', 1)
thdr.update('DC-FLAG', 0)
# wavelength axis header =============================
thdr.update('CTYPE1', 'LINEAR ')
thdr.update('LTV1', 1)
thdr.update('LTM1_1', 1.0)
thdr.update('CRPIX1', 1.0)
thdr.update('CDELT1', wave_step)
thdr.update('CRVAL1', wv1)
thdr.update('CD1_1', wave_step)
# slit-position axis header ==========================
thdr.update('CTYPE2', 'LINEAR ')
thdr.update('LTV2', 1)
thdr.update('LTM2_2', 1.0)
thdr.update('CRPIX2', 1)
thdr.update('CRVAL2', 1)
thdr.update('CD2_2', 1)
ip.savefits(outputfile, tstrip, header=thdr)
np.savetxt('.'.join(outputfile.split('.')[:-1])+'.wave', xwave)
'''plt.subplot(211)
plt.imshow(astrip, aspect=2)
plt.xlim(0,nx)
plt.subplot(212)
plt.imshow(tstrip, aspect=2)
plt.xlim(0,nwave)
plt.show()
'''
##2013-11-21 cksim inserted below draw_strips_file()
#draw_strips_file('.'.join(outputfile.split('.')[:-1])+'.fits', '.'.join(outputfile.split('.')[:-1])+'.wave', linefile='ohlines.dat', \
# target_path=outputfile.split('SDC')[0], desc='SDC'+outputfile.split('SDC')[1].split('.fits')[0])
return tstrip, thdr
def extract_strips(filename, band, apnum=[], pdeg=PDEGREE, \
PA=0, offset=[1023.5,1023.5], pscale=0.018, \
slit_len=[-1,1], slit_step=0.025, wave_step=0.00001, \
fitting_path=FITTING_PATH, \
target_path=ONESTEP_PATH):
'''
Extract the strips directly based on ZEMAX analysis fitting data
(using mapping parameters like position angle, pixel scale, ...
- input : for each band
1. FITTING DATA (fitting_path)
2. MAPPING DATA (PA,offset,pscale)
'''
fpath, fname = ip.split_path(filename)
if ip.exist_path(target_path) == False: target_path = fpath
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
img, hdr = ip.readfits(filename)
# read order information from file
onum, odesc, owv1, owv2 = ip.read_orderinfo(band)
if len(apnum) == 0:
apnum = range(len(onum))
# read image size
ny, nx = img.shape
#==============================================================================
# Extract strips based on ZEMAX fitting data
#==============================================================================
descs = []
strips = []
wavelengths = []
for k in apnum:
desc, wv1, wv2 = (odesc[k], owv1[k], owv2[k])
print "order # = %s, wrr = [%f, %f]" % (desc, wv1, wv2)
# read the echellogram fitting data
mx = np.loadtxt(FITTING_PATH+'mx_%s_%02d_%02d.dat' % (desc, pdeg[0], pdeg[1]))
my = np.loadtxt(FITTING_PATH+'my_%s_%02d_%02d.dat' % (desc, pdeg[0], pdeg[1]))
# make X dimension array (for wavelength)
twave = np.arange(wv1, wv2, wave_step, dtype=np.float64)
n_wave = len(twave)
# make Y dimension array (for slit)
tslit = np.arange(slit_len[0],slit_len[1]+slit_step, slit_step, dtype=np.float64)
n_slit = len(tslit)
# make 2D array for wavelength, slit-positions
swave = np.zeros([n_slit,n_wave], dtype=np.float64)
sslit = np.zeros([n_slit,n_wave], dtype=np.float64)
for i in range(n_wave):
sslit[:,i] = tslit
for i in range(n_slit):
swave[i,:] = twave
# find X, Y positions for each wavelength and slit-position
sx = ip.polyval2d(swave, sslit, mx, deg=pdeg)
sy = ip.polyval2d(swave, sslit, my, deg=pdeg)
# transform into pixel units
px, py = ip.xy2pix(sx, sy, PA=PA, offset=offset, pscale=pscale)
# check image range 0 < x < 2048
xmin, xmax = (0,n_wave)
for i in range(n_slit):
vv = np.where((px[i,:] >= 0) & (px[i,:] < nx))[0]
if np.min(vv) > xmin: xmin = np.min(vv)
if np.max(vv) < xmax: xmax = np.max(vv)
# extract the aperture by using interpolation from image
tstrip = ip.imextract(img, px[:,xmin:xmax], py[:,xmin:xmax])
twave = twave[xmin:xmax]
print ' + Wavelength valid range = [%f, %f]' % (twave[0], twave[-1])
descs.append(desc)
wavelengths.append(twave)
strips.append(tstrip)
#==============================================================================
# Save the strips in FITS format
#==============================================================================
for d, w, s in zip(descs, wavelengths, strips):
shdr = header.copy()
shdr.update('GEN-TIME', time.strftime('%Y-%m-%d %H:%M:%S'))
shdr.update('LNAME', lname)
shdr.update('ECH-ORD', d)
# WCS header ========================================
shdr.update('WAT0_001', 'system=world')
shdr.update('WAT1_001', 'wtype=linear label=Wavelength units=microns units_display=microns')
shdr.update('WAT2_001', 'wtype=linear')
shdr.update('WCSDIM', 2)
shdr.update('DISPAXIS', 1)
shdr.update('DC-FLAG', 0)
# wavelength axis header =============================
shdr.update('CTYPE1', 'LINEAR ')
shdr.update('LTV1', 1)
shdr.update('LTM1_1', 1.0)
shdr.update('CRPIX1', 1.0)
#header.update('CDELT1', w[1]-w[0])
shdr.update('CRVAL1', w[0])
shdr.update('CD1_1', w[1]-w[0])
# slit-position axis header ==========================
shdr.update('CTYPE2', 'LINEAR ')
shdr.update('LTV2', 1)
shdr.update('LTM2_2', 1.0)
shdr.update('CRPIX2', 1.0)
#header.update('CDELT1', w[1]-w[0])
shdr.update('CRVAL2', -1.0)
shdr.update('CD2_2', slit_step)
# save FITS with header
ip.savefits(EXTRACT_PATH+'IGRINS_%s_%s.fits' % (lname,d), s, header=shdr)
np.savetxt(EXTRACT_PATH+'IGRINS_%s_%s.wave' % (lname,d), w)
def line_identify(stripfile, linedata=[], outputfile=None, \
npoints=30, spix=5, dpix=5, thres=15000):
'''
Identify the lines in the strip based on the line database
- inputs :
1. stripfile (with wavelength data or not)
2. linefile (for line database)
'''
def key_press(event):
ax = event.inaxes
if ax == None: return
ax_title = ax.get_title()
if event.key == 'q': plt.close('all')
if event.key == 'm':
click_x, click_y = event.xdata, event.ydata
rr = np.arange((x2-2*dpix),(x2+2*dpix+1), dtype=np.int)
#p = ip.gauss_fit(rr, row[rr], p0=[1, x2, 1])
#a2.plot(rr, ip.gauss(rr, *p), 'r--')
#mx = p[1]
mx, mval = ip.find_features(rr, row[rr], gpix=dpix)
mx, mval = mx[0], mval[0]
a2.plot(mx, mval, 'ro')
fig.canvas.draw()
fwv = cwv[np.argmin(np.abs(cwv-wav[mx]))]
strtmp = raw_input('input wavelength at (%d, %d) = %.7f:' % (mx, my, fwv))
if strtmp == '': strtmp = fwv
try:
mwv = np.float(strtmp)
lxx.append(mx)
lyy.append(my)
lwv.append(mwv)
a1.plot(mx, my, 'ro')
fig.canvas.draw()
print '%.7f at (%d, %d)' % (mwv, mx, my)
except:
print 'No input, again...'
if len(linedata) == 2:
cwv, cflx = linedata
else:
print 'No input data for line information'
cwv, cflx = None, None
strip, hdr = ip.readfits(stripfile)
fpath, fname = ip.split_path(stripfile)
if outputfile == None: outputfile = fpath+'c'+fname
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
ny, nx = strip.shape
yy, xx = np.indices(strip.shape)
if 'WV-DIM' in hdr.keys():
xdim, ydim = np.array(hdr.get('WV-DIM').split(','), dtype=np.int)
wl_coeff = np.zeros([xdim*ydim])
for i in range(xdim):
tmp = hdr.get('WV-X%03d' % (i,))
wl_coeff[(i*ydim):(i*ydim+ydim)] = np.array(tmp.split(','), dtype=np.double)
awave = ip.polyval2d(xx, yy, wl_coeff, deg=[xdim-1, ydim-1])
else:
print 'No wavelength data in FITS header'
awave = None
# define figure object
fig = plt.figure(figsize=(14,7))
a1 = fig.add_subplot(211, title='strip')
a2 = fig.add_subplot(212, title='line')
# draw the strip image
z1, z2 = ip.zscale(strip)
a1.imshow(strip, cmap='gray',vmin=z1, vmax=z2, aspect='auto')
a1.set_xlim(0,nx)
a1.set_ylim(-10,ny+10)
lspec = np.sum(strip, axis=0)
lxpos = np.arange(nx)
a2.plot(lxpos, lspec)
a2.set_xlim(0,nx)
# draw the lines in the database
if (awave != None) & (cwv != None):
twave = awave[int(ny/2),:]
print twave
wv1, wv2 = np.min(twave), np.max(twave)
for wv0 in cwv[(cwv > wv1) & (cwv < wv2)]:
x0 = np.argmin(np.abs(twave-wv0))
a2.plot([x0, x0], [0, ny], 'r--', linewidth=1, alpha=0.4)
# make the array for emission feature points
lxx, lyy, lwave = ([], [], [])
fig.canvas.mpl_connect('key_press_event', key_press)
print '[m] mark the line and input the wavelength'
print '[q] quit from this aperture'
plt.show()
return
def extract_ap(img, apfiles, wlfiles=None, header=None, ap_width=60):
'''
Extract the apertures using ap_tracing solution and wavelength data files
- INPUTS :
1. img (input 2D image data)
2. apfiles (a list of input ap_tracing files)
3. wlfiles (a list of wavelength fitting coefficient files)
4. ap_width (to be extracted with this pixel width)
- OUTPUTS :
1. strips (output 2D strip image data)
2. waves (output 2D wavelength data for the strip)
3. hdrs (output FITS header for 2D strip image)
'''
# read image size
ny, nx = img.shape
#ap_width=60 #just for test on 2013-08-30
ostrips, owaves, ohdrs = [], [], []
for k, apfile in enumerate(apfiles): #
#===========================================================
# extract the strip with a regular width
#===========================================================
ap_coeff = np.loadtxt(apfile)
# extract the aperture number from file name
ap_num = int(apfile.split('.')[-2])
# read the wavelength fitting coefficients
if wlfiles != None:
wl_coeff = np.loadtxt(wlfiles[k])
wtmp = wlfiles[k].split('.')[-3].split('_')
#print wtmp
# find the dimension of 2d fitting coefficients
xdim, ydim = int(wtmp[2])+1, int(wtmp[3])+1
# find the ap_tracing mode
ap_mode = wtmp[0]
else:
ap_mode = ''
wl_coeff = None
# calculate the x, y positions of aperture bottom curve
xpos = np.arange(nx)
sparepixels = 5
#if ap_num >= 0 and ap_num <=8 : sparepixels = 20
#elif ap_num >= 9 and ap_num <=18 : sparepixels = 7
#else : sparepixels = 5
#sparepixels = 0 #just for test (to fix)
# bottom curve
#ypos = np.polynomial.polyval(xpos, ap_coeff[0,:]) #for numpy version lower than 1.7.0
ypos = np.polynomial.polynomial.polyval(xpos, ap_coeff[0,:]) -sparepixels #for numpy version higher than or equal to 1.7.0
#bottomcurve, = plt.plot(range(0,nx),ypos)
# top curve
#ypos_top = np.polynomial.polyval(xpos, ap_coeff[1,:])#for numpy version lower than 1.7.0
ypos_top = np.polynomial.polynomial.polyval(xpos, ap_coeff[1,:]) + sparepixels#for numpy version higher than or equal to 1.7.0
# make 2D strip array
#ap_width = np.average(ypos_top - ypos)
if k>=0 and k<=9:
ap_width = 70
elif k>9 and k<=17:
ap_width = 65
else:
ap_width = 63
strip = np.zeros([ap_width,nx], dtype=np.double)
# generate the coordinate array for strip
yy, xx = np.indices(strip.shape)
# add the y-direction aperture curve to the y-coordinates of strip
ap_yy = np.array(yy, dtype=np.double) + ypos
ap_xx = np.array(xx, dtype=np.double)
# convert positions into integer indices of aperture positions
#iyy = np.array(np.floor(ap_yy), dtype=np.int) #we use "round" 2013-09-03 meeting with SPak & Huynh Anh
iyy = np.array(np.round(ap_yy), dtype=np.int)
# calculate the fraction subtracted by integer pixel index
fyy = ap_yy - iyy
# find the valid points
vv = np.where((iyy >= 0) & (iyy <= ny-2))
# input the value into the strip
#we use "round" 2013-09-03 meeting with SPak & Huynh Anh
#and we don't scale or interpolate pixel intensities 2013-09-03 meeting with SPak & Huynh Anh
#strip[yy[vv],xx[vv]] = \
# img[iyy[vv],xx[vv]] * (1.0 - fyy[yy[vv],xx[vv]]) + \
# img[(iyy[vv]+1),xx[vv]] * fyy[yy[vv],xx[vv]]
strip[yy[vv],xx[vv]] = img[iyy[vv],xx[vv]]
#===========================================================
# update the FITS header
#===========================================================
if header != None:
hdr = header.copy()
#hdr.update('AP-MODE',ap_mode)
hdr.update('AP-NUM', ap_num)
c1list = []
for c in ap_coeff[0,:]:
c1list.append('%.8E' % (c,))
hdr.update('AP-COEF1', ','.join(c1list))
c2list = []
for c in ap_coeff[1,:]:
c2list.append('%.8E' % (c,))
hdr.update('AP-COEF2', ','.join(c2list))
hdr.update('AP-WIDTH', ap_width)
# input the wavelength solution for a strip
if wl_coeff != None:
hdr.update('WV-DIM', '%d,%d' % (xdim, ydim))
for i in range(xdim):
wllist = []
for c in wl_coeff[(i*(ydim)):(i*ydim+ydim)]:
wllist.append('%.8E' % (c,))
hdr.update('WV-X%03d' % (i,), ','.join(wllist))
wave = ip.polyval2d(xx, yy, wl_coeff, deg=[(xdim-1), (ydim-1)])
else:
wave = None
hdr = None
ostrips.append(strip)
owaves.append(wave)
ohdrs.append(hdr)
return ostrips, owaves, ohdrs
def line_identify(stripfile, linedata=[], outputfile=None, \
npoints=30, spix=5, dpix=5, thres=15000):
'''
Identify the lines in the strip based on the line database
- inputs :
1. stripfile (with wavelength data or not)
2. linefile (for line database)
'''
def key_press(event):
ax = event.inaxes
if ax == None: return
ax_title = ax.get_title()
if event.key == 'q': plt.close('all')
if event.key == 'm':
click_x, click_y = event.xdata, event.ydata
rr = np.arange((click_x - 2 * dpix), (click_x + 2 * dpix + 1),
dtype=np.int)
#p = ip.gauss_fit(rr, row[rr], p0=[1, x2, 1])
#a2.plot(rr, ip.gauss(rr, *p), 'r--')
#mx = p[1]
mx, mval = ip.find_features(rr, row[rr], gpix=dpix)
mx, mval = mx[0], mval[0]
a2.plot(mx, mval, 'ro')
fig.canvas.draw()
fwv = cwv[np.argmin(np.abs(cwv - wav[mx]))]
strtmp = raw_input('input wavelength at (%d, %d) = %.7f:' %
(mx, my, fwv))
if strtmp == '': strtmp = fwv
try:
mwv = np.float(strtmp)
lxx.append(mx)
lyy.append(my)
lwv.append(mwv)
a1.plot(mx, my, 'ro')
fig.canvas.draw()
print '%.7f at (%d, %d)' % (mwv, mx, my)
except:
print 'No input, again...'
if len(linedata) == 2:
cwv, cflx = linedata
else:
print 'No input data for line information'
cwv, cflx = None, None
strip, hdr = ip.readfits(stripfile)
fpath, fname = ip.split_path(stripfile)
if outputfile == None: outputfile = fpath + 'c' + fname
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
ny, nx = strip.shape
yy, xx = np.indices(strip.shape)
if 'WV-DIM' in hdr.keys():
xdim, ydim = np.array(hdr.get('WV-DIM').split(','), dtype=np.int)
wl_coeff = np.zeros([xdim * ydim])
for i in range(xdim):
tmp = hdr.get('WV-X%03d' % (i, ))
wl_coeff[(i * ydim):(i * ydim + ydim)] = np.array(tmp.split(','),
dtype=np.double)
awave = ip.polyval2d(xx, yy, wl_coeff, deg=[xdim - 1, ydim - 1])
else:
print 'No wavelength data in FITS header'
awave = None
# define figure object
fig = plt.figure(figsize=(14, 7))
a1 = fig.add_subplot(211, title='strip')
a2 = fig.add_subplot(212, title='line')
# draw the strip image
z1, z2 = ip.zscale(strip)
a1.imshow(strip, cmap='gray', vmin=z1, vmax=z2, aspect='auto')
a1.set_xlim(0, nx)
a1.set_ylim(-10, ny + 10)
lspec = np.sum(strip, axis=0)
lxpos = np.arange(nx)
a2.plot(lxpos, lspec)
a2.set_xlim(0, nx)
# draw the lines in the database
if (awave != None) & (cwv != None):
twave = awave[int(ny / 2), :]
print twave
wv1, wv2 = np.min(twave), np.max(twave)
for wv0 in cwv[(cwv > wv1) & (cwv < wv2)]:
x0 = np.argmin(np.abs(twave - wv0))
a2.plot([x0, x0], [0, ny], 'r--', linewidth=1, alpha=0.4)
# make the array for emission feature points
lxx, lyy, lwave = ([], [], [])
fig.canvas.mpl_connect('key_press_event', key_press)
print '[m] mark the line and input the wavelength'
print '[q] quit from this aperture'
plt.show()
return
def transform_ap_file(stripfile,
wave_step=False,
outputfile=None): #2014-01-13 cksim
'''
Apply linear interpolation to the strip with a regular wavelength
- INPUTS :
1. stripfile (FITS)
2. wave_step (to be extracted with this wavelength step for a pixel)
3. outputfile (FITS filename)
- OUTPUTS:
1. tranformed 2D strip data with header
'''
astrip, ahdr = ip.readfits(stripfile)
fpath, fname = ip.split_path(stripfile)
if outputfile == None: outputfile = fpath + fname + '.tr'
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
ny, nx = astrip.shape
yy, xx = np.indices(astrip.shape)
if 'WV-DIM' in ahdr.keys():
xdim, ydim = np.array(ahdr.get('WV-DIM').split(','), dtype=np.int)
wl_coeff = np.zeros([xdim * ydim])
for i in range(xdim):
tmp = ahdr.get('WV-X%03d' % (i, ))
wl_coeff[(i * ydim):(i * ydim + ydim)] = np.array(tmp.split(','),
dtype=np.double)
awave = ip.polyval2d(xx, yy, wl_coeff, deg=[xdim - 1, ydim - 1])
else:
print 'No wavelength data in FITS header'
return None, None
if wave_step == False:
wave_step = (
(np.max(awave) - np.min(awave))) / (nx - 1) #2013-01-14 cksim
#--new version--
tstrip, xwave = transform_ap(astrip, awave, wave_step=wave_step)
wv1, wv2 = np.min(xwave), np.max(xwave)
'''old version
wv1, wv2 = (np.min(awave), np.max(awave))
xwave = np.arange(wv1, wv2, wave_step)
nwave = len(xwave)
#print nx, ny, nwave, np.min(awave), np.max(awave)
tstrip = np.zeros([ny,nwave])
for i in range(ny):
row = astrip[i,:]
wv = awave[i,:]
xrow = np.interp(xwave, wv, row)
tstrip[i,:] = xrow
'''
thdr = ahdr.copy()
thdr.update('TRN-TIME', time.strftime('%Y-%m-%d %H:%M:%S'))
# WCS header ========================================
thdr.update('WAT0_001', 'system=world')
thdr.update(
'WAT1_001',
'wtype=linear label=Wavelength units=microns units_display=microns')
thdr.update('WAT2_001', 'wtype=linear')
thdr.update('WCSDIM', 2)
thdr.update('DISPAXIS', 1)
thdr.update('DC-FLAG', 0)
# wavelength axis header =============================
thdr.update('CTYPE1', 'LINEAR ')
thdr.update('LTV1', 1)
thdr.update('LTM1_1', 1.0)
thdr.update('CRPIX1', 1.0)
thdr.update('CDELT1', wave_step)
thdr.update('CRVAL1', wv1)
thdr.update('CD1_1', wave_step)
# slit-position axis header ==========================
thdr.update('CTYPE2', 'LINEAR ')
thdr.update('LTV2', 1)
thdr.update('LTM2_2', 1.0)
thdr.update('CRPIX2', 1)
thdr.update('CRVAL2', 1)
thdr.update('CD2_2', 1)
ip.savefits(outputfile, tstrip, header=thdr)
np.savetxt('.'.join(outputfile.split('.')[:-1]) + '.wave', xwave)
'''plt.subplot(211)
plt.imshow(astrip, aspect=2)
plt.xlim(0,nx)
plt.subplot(212)
plt.imshow(tstrip, aspect=2)
plt.xlim(0,nwave)
plt.show()
'''
##2013-11-21 cksim inserted below draw_strips_file()
#draw_strips_file('.'.join(outputfile.split('.')[:-1])+'.fits', '.'.join(outputfile.split('.')[:-1])+'.wave', linefile='ohlines.dat', \
# target_path=outputfile.split('SDC')[0], desc='SDC'+outputfile.split('SDC')[1].split('.fits')[0])
return tstrip, thdr
def extract_strips(filename, band, apnum=[], pdeg=PDEGREE, \
PA=0, offset=[1023.5,1023.5], pscale=0.018, \
slit_len=[-1,1], slit_step=0.025, wave_step=0.00001, \
fitting_path=FITTING_PATH, \
target_path=ONESTEP_PATH):
'''
Extract the strips directly based on ZEMAX analysis fitting data
(using mapping parameters like position angle, pixel scale, ...
- input : for each band
1. FITTING DATA (fitting_path)
2. MAPPING DATA (PA,offset,pscale)
'''
fpath, fname = ip.split_path(filename)
if ip.exist_path(target_path) == False: target_path = fpath
# extract the file name only without extension
name = '.'.join(fname.split('.')[:-1])
img, hdr = ip.readfits(filename)
# read order information from file
onum, odesc, owv1, owv2 = ip.read_orderinfo(band)
if len(apnum) == 0:
apnum = range(len(onum))
# read image size
ny, nx = img.shape
#==============================================================================
# Extract strips based on ZEMAX fitting data
#==============================================================================
descs = []
strips = []
wavelengths = []
for k in apnum:
desc, wv1, wv2 = (odesc[k], owv1[k], owv2[k])
print "order # = %s, wrr = [%f, %f]" % (desc, wv1, wv2)
# read the echellogram fitting data
mx = np.loadtxt(FITTING_PATH + 'mx_%s_%02d_%02d.dat' %
(desc, pdeg[0], pdeg[1]))
my = np.loadtxt(FITTING_PATH + 'my_%s_%02d_%02d.dat' %
(desc, pdeg[0], pdeg[1]))
# make X dimension array (for wavelength)
twave = np.arange(wv1, wv2, wave_step, dtype=np.float64)
n_wave = len(twave)
# make Y dimension array (for slit)
tslit = np.arange(slit_len[0],
slit_len[1] + slit_step,
slit_step,
dtype=np.float64)
n_slit = len(tslit)
# make 2D array for wavelength, slit-positions
swave = np.zeros([n_slit, n_wave], dtype=np.float64)
sslit = np.zeros([n_slit, n_wave], dtype=np.float64)
for i in range(n_wave):
sslit[:, i] = tslit
for i in range(n_slit):
swave[i, :] = twave
# find X, Y positions for each wavelength and slit-position
sx = ip.polyval2d(swave, sslit, mx, deg=pdeg)
sy = ip.polyval2d(swave, sslit, my, deg=pdeg)
# transform into pixel units
px, py = ip.xy2pix(sx, sy, PA=PA, offset=offset, pscale=pscale)
# check image range 0 < x < 2048
xmin, xmax = (0, n_wave)
for i in range(n_slit):
vv = np.where((px[i, :] >= 0) & (px[i, :] < nx))[0]
if np.min(vv) > xmin: xmin = np.min(vv)
if np.max(vv) < xmax: xmax = np.max(vv)
# extract the aperture by using interpolation from image
tstrip = ip.imextract(img, px[:, xmin:xmax], py[:, xmin:xmax])
twave = twave[xmin:xmax]
print ' + Wavelength valid range = [%f, %f]' % (twave[0], twave[-1])
descs.append(desc)
wavelengths.append(twave)
strips.append(tstrip)
#==============================================================================
# Save the strips in FITS format
#==============================================================================
for d, w, s in zip(descs, wavelengths, strips):
shdr = header.copy()
shdr.update('GEN-TIME', time.strftime('%Y-%m-%d %H:%M:%S'))
shdr.update('LNAME', lname)
shdr.update('ECH-ORD', d)
# WCS header ========================================
shdr.update('WAT0_001', 'system=world')
shdr.update(
'WAT1_001',
'wtype=linear label=Wavelength units=microns units_display=microns'
)
shdr.update('WAT2_001', 'wtype=linear')
shdr.update('WCSDIM', 2)
shdr.update('DISPAXIS', 1)
shdr.update('DC-FLAG', 0)
# wavelength axis header =============================
shdr.update('CTYPE1', 'LINEAR ')
shdr.update('LTV1', 1)
shdr.update('LTM1_1', 1.0)
shdr.update('CRPIX1', 1.0)
#header.update('CDELT1', w[1]-w[0])
shdr.update('CRVAL1', w[0])
shdr.update('CD1_1', w[1] - w[0])
# slit-position axis header ==========================
shdr.update('CTYPE2', 'LINEAR ')
shdr.update('LTV2', 1)
shdr.update('LTM2_2', 1.0)
shdr.update('CRPIX2', 1.0)
#header.update('CDELT1', w[1]-w[0])
shdr.update('CRVAL2', -1.0)
shdr.update('CD2_2', slit_step)
# save FITS with header
ip.savefits(EXTRACT_PATH + 'IGRINS_%s_%s.fits' % (lname, d),
s,
header=shdr)
np.savetxt(EXTRACT_PATH + 'IGRINS_%s_%s.wave' % (lname, d), w)
def extract_ap(img, apfiles, wlfiles=None, header=None, ap_width=60):
'''
Extract the apertures using ap_tracing solution and wavelength data files
- INPUTS :
1. img (input 2D image data)
2. apfiles (a list of input ap_tracing files)
3. wlfiles (a list of wavelength fitting coefficient files)
4. ap_width (to be extracted with this pixel width)
- OUTPUTS :
1. strips (output 2D strip image data)
2. waves (output 2D wavelength data for the strip)
3. hdrs (output FITS header for 2D strip image)
'''
# read image size
ny, nx = img.shape
#ap_width=60 #just for test on 2013-08-30
ostrips, owaves, ohdrs = [], [], []
for k, apfile in enumerate(apfiles): #
#===========================================================
# extract the strip with a regular width
#===========================================================
ap_coeff = np.loadtxt(apfile)
# extract the aperture number from file name
ap_num = int(apfile.split('.')[-2])
# read the wavelength fitting coefficients
if wlfiles != None:
wl_coeff = np.loadtxt(wlfiles[k])
wtmp = wlfiles[k].split('.')[-3].split('_')
#print wtmp
# find the dimension of 2d fitting coefficients
xdim, ydim = int(wtmp[2]) + 1, int(wtmp[3]) + 1
# find the ap_tracing mode
ap_mode = wtmp[0]
else:
ap_mode = ''
wl_coeff = None
# calculate the x, y positions of aperture bottom curve
xpos = np.arange(nx)
sparepixels = 5
#if ap_num >= 0 and ap_num <=8 : sparepixels = 20
#elif ap_num >= 9 and ap_num <=18 : sparepixels = 7
#else : sparepixels = 5
#sparepixels = 0 #just for test (to fix)
# bottom curve
#ypos = np.polynomial.polyval(xpos, ap_coeff[0,:]) #for numpy version lower than 1.7.0
ypos = np.polynomial.polynomial.polyval(
xpos, ap_coeff[0, :]
) - sparepixels #for numpy version higher than or equal to 1.7.0
#bottomcurve, = plt.plot(range(0,nx),ypos)
# top curve
#ypos_top = np.polynomial.polyval(xpos, ap_coeff[1,:])#for numpy version lower than 1.7.0
ypos_top = np.polynomial.polynomial.polyval(
xpos, ap_coeff[1, :]
) + sparepixels #for numpy version higher than or equal to 1.7.0
# make 2D strip array
#ap_width = np.average(ypos_top - ypos)
if k >= 0 and k <= 9:
ap_width = 70
elif k > 9 and k <= 17:
ap_width = 65
else:
ap_width = 63
strip = np.zeros([ap_width, nx], dtype=np.double)
# generate the coordinate array for strip
yy, xx = np.indices(strip.shape)
# add the y-direction aperture curve to the y-coordinates of strip
ap_yy = np.array(yy, dtype=np.double) + ypos
ap_xx = np.array(xx, dtype=np.double)
# convert positions into integer indices of aperture positions
#iyy = np.array(np.floor(ap_yy), dtype=np.int) #we use "round" 2013-09-03 meeting with SPak & Huynh Anh
iyy = np.array(np.round(ap_yy), dtype=np.int)
# calculate the fraction subtracted by integer pixel index
fyy = ap_yy - iyy
# find the valid points
vv = np.where((iyy >= 0) & (iyy <= ny - 2))
# input the value into the strip
#we use "round" 2013-09-03 meeting with SPak & Huynh Anh
#and we don't scale or interpolate pixel intensities 2013-09-03 meeting with SPak & Huynh Anh
#strip[yy[vv],xx[vv]] = \
# img[iyy[vv],xx[vv]] * (1.0 - fyy[yy[vv],xx[vv]]) + \
# img[(iyy[vv]+1),xx[vv]] * fyy[yy[vv],xx[vv]]
strip[yy[vv], xx[vv]] = img[iyy[vv], xx[vv]]
#===========================================================
# update the FITS header
#===========================================================
if header != None:
hdr = header.copy()
#hdr.update('AP-MODE',ap_mode)
hdr.update('AP-NUM', ap_num)
c1list = []
for c in ap_coeff[0, :]:
c1list.append('%.8E' % (c, ))
hdr.update('AP-COEF1', ','.join(c1list))
c2list = []
for c in ap_coeff[1, :]:
c2list.append('%.8E' % (c, ))
hdr.update('AP-COEF2', ','.join(c2list))
hdr.update('AP-WIDTH', ap_width)
# input the wavelength solution for a strip
if wl_coeff != None:
hdr.update('WV-DIM', '%d,%d' % (xdim, ydim))
for i in range(xdim):
wllist = []
for c in wl_coeff[(i * (ydim)):(i * ydim + ydim)]:
wllist.append('%.8E' % (c, ))
hdr.update('WV-X%03d' % (i, ), ','.join(wllist))
wave = ip.polyval2d(xx,
yy,
wl_coeff,
deg=[(xdim - 1), (ydim - 1)])
else:
wave = None
hdr = None
ostrips.append(strip)
owaves.append(wave)
ohdrs.append(hdr)
return ostrips, owaves, ohdrs