def test4(band, lname='ohlines'):
if band == 'H':
ap_num = 23
else:
ap_num = 20
cwv, cflx = ip.read_lines(lname+'.dat')
for k in range(ap_num):
strdesc = 'IGRINS_%s_%s.%03d' % (band, lname, k)
strip, hdr = ip.readfits(MANUAL_PATH+strdesc+'.fits')
z1, z2 = ip.zscale(strip)
f2 = plt.figure(2,figsize=(12,5),dpi=200)
a1 = f2.add_subplot(211, aspect='auto')
ny, nx = strip.shape
a1.imshow(strip, cmap='hot', aspect=nx/1000.0, vmin=z1, vmax=z2)
a1.set_xlim((0,nx))
a1.set_ylim((0,ny))
a1.set_title('%s' % (strdesc,))
f2.savefig(PNG_PATH+strdesc+'.png')
strdesc = 'tIGRINS_%s_%s.%03d' % (band, lname, k)
strip, hdr = ip.readfits(MANUAL_PATH+strdesc+'.fits')
wave = np.loadtxt(MANUAL_PATH+strdesc+'.wave')
draw_strips(strip, wave, desc=strdesc, linedata=[cwv, cflx])
def test4(band, lname='ohlines'):
if band == 'H':
ap_num = 23
else:
ap_num = 20
cwv, cflx = ip.read_lines(lname + '.dat')
for k in range(ap_num):
strdesc = 'IGRINS_%s_%s.%03d' % (band, lname, k)
strip, hdr = ip.readfits(MANUAL_PATH + strdesc + '.fits')
z1, z2 = ip.zscale(strip)
f2 = plt.figure(2, figsize=(12, 5), dpi=200)
a1 = f2.add_subplot(211, aspect='auto')
ny, nx = strip.shape
a1.imshow(strip, cmap='hot', aspect=nx / 1000.0, vmin=z1, vmax=z2)
a1.set_xlim((0, nx))
a1.set_ylim((0, ny))
a1.set_title('%s' % (strdesc, ))
f2.savefig(PNG_PATH + strdesc + '.png')
strdesc = 'tIGRINS_%s_%s.%03d' % (band, lname, k)
strip, hdr = ip.readfits(MANUAL_PATH + strdesc + '.fits')
wave = np.loadtxt(MANUAL_PATH + strdesc + '.wave')
draw_strips(strip, wave, desc=strdesc, linedata=[cwv, cflx])
def test2(band, lname='ohlines'):
'''
Draw the original image
'''
timg, thdr = ip.readfits(IMAGE_PATH + 'IGRINS_%s_%s.fits' % (band, lname))
z1, z2 = ip.zscale(timg, contrast=0.2)
f1 = plt.figure(1, figsize=(12, 12), dpi=200)
a1 = f1.add_subplot(111, aspect='equal')
a1.imshow(timg, cmap='hot', vmin=z1, vmax=z2)
a1.set_xlim((0, 2048))
a1.set_ylim((0, 2048))
a1.set_title('IGRINS %s band - %s (simulated)' % (band, lname))
a1.set_xlabel('X [pixel]')
a1.set_ylabel('Y [pixel]')
f1.savefig(PNG_PATH + 'IGRINS_%s_%s.png' % (band, lname))
plt.close('all')
def test2(band, lname='ohlines'):
'''
Draw the original image
'''
timg, thdr = ip.readfits(IMAGE_PATH+'IGRINS_%s_%s.fits' % (band,lname))
z1, z2 = ip.zscale(timg, contrast=0.2)
f1 = plt.figure(1,figsize=(12,12),dpi=200)
a1 = f1.add_subplot(111, aspect='equal')
a1.imshow(timg, cmap='hot', vmin=z1, vmax=z2)
a1.set_xlim((0,2048))
a1.set_ylim((0,2048))
a1.set_title('IGRINS %s band - %s (simulated)' % (band,lname))
a1.set_xlabel('X [pixel]')
a1.set_ylabel('Y [pixel]')
f1.savefig(PNG_PATH+'IGRINS_%s_%s.png' % (band,lname))
plt.close('all')
def draw_strips(strip, wave, desc='', linedata=[], lampname='', grayplot=False, \
target_path=PNG_PATH):
'''
Draw the strips with wavelength
- INPUTS:
1. strip data
2. wavelength data
3. line data
- OUTPUTS:
PNG files
'''
#print 'draw_strips', lampname
if len(linedata) > 0:
cwv, cflx = linedata
wmin, wmax = (np.min(wave), np.max(wave))
z1, z2 = ip.zscale(strip)
f2 = plt.figure(2,figsize=(12,5),dpi=200)
a1 = f2.add_subplot(211, aspect='auto')
a2 = f2.add_subplot(212, aspect='auto')
ny, nx = strip.shape
cuty = ny/2-8
a1.imshow(strip, cmap='hot', aspect=nx/1000.0, vmin=z1, vmax=z2)
a1.plot([0,nx],[cuty,cuty], 'g--', alpha=0.8, linewidth=3)
a1.set_xlim((0,nx))
a1.set_ylim((0,ny))
a1.set_title('%s' % (desc,))
a2.plot(wave, strip[cuty,:], 'b-', linewidth=1)
ww = np.where((cwv < wmax) & (cwv > wmin))[0]
fmax = np.zeros([len(ww)]) + np.max(strip[cuty,:])*1.05
a2.plot(cwv[ww], fmax, 'r|', markersize=10, markeredgewidth=2, alpha=0.7 )
if lampname != '': lampname = '('+lampname+')'
a2.set_title('%s %s' % (desc,lampname))
a2.set_xlabel('Wavelength [um]')
a2.set_xlim((wmin, wmax))
a2.set_ylim((0, fmax[0]*1.1))
# f2.savefig(target_path+'%s_prof.png' % (desc,)) #2013-11-21 cksim commented this
f2.savefig(target_path+'%s.png' % (desc,)) #2013-11-21 cksim
if grayplot == True:
f3 = plt.figure(3, figsize=(12,5),dpi=200)
a3 = f3.add_subplot(111)
a3.imshow(strip, cmap='gray', aspect=nx/200.0, vmin=z1, vmax=z2)
x, y = (np.arange(nx), np.sum(strip, axis=0))
a3.plot(x, (y-np.min(y))/(np.max(y)-np.min(y))*ny*0.9,\
'b-', linewidth=3, alpha=0.7)
x, y = ( (cwv[ww]-wmin)/(wmax-wmin)*(nx-1), np.zeros(len(ww))+ny*1.05)
a3.plot(x, y, 'r|', markersize=10, markeredgewidth=2, alpha=0.7)
a3.set_xlim((0,nx))
a3.set_ylim((0,ny*1.1))
cticks = wticks[np.where((wticks > wmin) & (wticks < wmax))]
xticks = (cticks-wmin)/(wmax-wmin)*(nx-1)
#print xticks
a3.set_yticks([])
a3.set_xticks(xticks)
a3.set_xticklabels(['%.3f' % x for x in cticks])
a3.set_xlabel('Wavelength [um]')
f3.savefig(target_path+'%s_gray.png' % (desc,))
plt.close('all')
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 _line_identify_old(stripfile, linefile=None, \
npoints=30, spix=4, dpix=5, thres=13000, fdeg=5, desc=''):
def key_press(event):
if event.key == 'q': plt.close('all')
if event.key == 'a':
line_idx = np.argmin( (event.xdata - ysignal)**2 )
line_x = ysignal[line_idx]
print line_idx, line_x
# mark the points for fitting
ll, = np.where((xx < line_x+dpix) & (xx > line_x-dpix))
print len(ll)
l1 = ax.plot([line_x, line_x], [0,ny], 'r-', linewidth=5, alpha=0.5)
l2 = ax.plot(xx[ll], yy[ll], 'ro')
coeff = np.polynomial.polynomial.polyfit(xx[ll],yy[ll],fdeg)
fig.canvas.draw()
print coeff
ycoeff[line_idx,:] = np.array(coeff)
# redraw for the marked points
# read the wavelength for this line
input = raw_input('input wavelength:')
try:
line_wv = np.float(input)
except:
line_wv = 0.0
print line_idx, line_x, line_wv
ywave[line_idx] = line_wv
strip, hdr = ip.readfits(stripfile)
ny, nx = strip.shape
z1, z2 = ip.zscale(strip)
# fitting the base level
snr = 10
ysum = np.average(strip[(ny/2-spix):(ny/2+spix),:], axis=0)
ll = np.arange(nx)
nrejt = 0
while (1):
yc = np.polynomial.polynomial.polyfit(ll, ysum[ll], fdeg)
yfit = np.polynomial.polynomial.polyval(np.arange(nx), yc)
ll, = np.where(ysum < yfit*(1.0 + 1.0/snr))
#print nrejt
if nrejt == len(ll): break
nrejt = len(ll)
ysignal = np.array(peak_find(ysum, thres=thres, dpix=dpix ))
# define figure object
fig = plt.figure(figsize=(14,4))
ax = fig.add_subplot(111)
# draw the strip image
ax.imshow(strip, cmap='gray',vmin=z1, vmax=z2, aspect='auto')
ax.set_xlim(0,nx)
ax.set_ylim(-5,ny+5)
# mark the number of lines
for i, ypeak in enumerate(ysignal):
if i % 2 == 1:
ytext = ny
else:
ytext = -5
ax.text(ypeak, ytext, i+1, fontsize=15)
# find the emission feature in each row
ysteps = np.linspace(spix, ny-spix, npoints)
# make the array for emission feature points
xx, yy = ([], [])
for ypos in ysteps:
irow = np.mean(strip[(ypos-spix/2):(ypos+spix/2),:],axis=0)
#a2.plot(irow)
# find the peak positions
xpos_list = peak_find(irow, dpix=dpix, thres=thres)
# draw and save the peak positions (x, y)
for xpos in xpos_list:
ax.plot(xpos, ypos, 'go', markersize=5, alpha=0.5)
xx.append(xpos)
yy.append(ypos)
# convert into the numpy array
xx = np.array(xx, dtype=np.float)
yy = np.array(yy, dtype=np.float)
# generate the wavelength array for each line
ywave = np.zeros(len(ysignal))
ycoeff = np.zeros([len(ysignal),fdeg+1])
fig.canvas.mpl_connect('key_press_event', key_press)
print '[a] add line and input wavelength'
print '[r] reset'
print '[q] quit from this aperture'
plt.show()
print 'thanks'
def ap_tracing_strip(band, filename, npoints=40, spix=10, dpix=20, thres=14000, \
start_col=None, ap_thres=None, degree=None, \
devide=8.0, target_path=MANUAL_PATH):
'''
Trace the apertures starting at "start_col" position (for FLAT spectrum)
- inputs
0. band
1. npoints : slicing number along the column direction
2. spix : summing pixel size along vertical column for finding strips
3. dpix : detecting pixel range of feature to be regarded as the same
4. thres : detecting intensity level for emission features
5. start_col : starting column number for tracing
6. ap_thres : threshold of pixel range to identify nearby aperture features
7. degree : degree of polynomial fitting
- outputs
1. coefficients of polynomial fittings
for start position of each aperture on y-axis
2. coefficients of polynomial fittings
for end position of each aperture on y-axis
'''
img, hdr = ip.readfits(filename)
img, hdr = ip.readfits(filename)
fpath, fname = ip.split_path(filename)
if ip.exist_path(target_path) == False: target_path = fpath
name = '.'.join(fname.split('.')[:-1])
# image size
ny, nx = img.shape
# define the threshold pixel range to be matched with nearby aperture positions
if ap_thres == None: ap_thres= nx/npoints/4
# define the degree of polynomials for fitting
if degree == None: degree = 3 #7
# find the apertures in the middle column
#if start_col == None: start_col = start_col #1500 #nx/2
icol = np.mean(img[:,(start_col-spix/2):(start_col+spix/2)], axis=1)
#print 'icol', icol, len(icol)
mcaps1, mcaps2 = strip_find(band, icol)
n_ap = len(mcaps1)
# make set of (x, y) positions for each aperture
# add the (x, y) positions at default column
apx1, apx2 = [], []
apy1, apy2 = [], []
for mcap1, mcap2 in zip(mcaps1, mcaps2):
apx1.append([start_col])
apx2.append([start_col])
apy1.append([mcap1])
apy2.append([mcap2])
# define the tracing direction (left, right)
xsteps = np.linspace(spix,nx-spix,npoints)
xlefts = xsteps[(xsteps < start_col)]
xrights = xsteps[(xsteps > start_col)]
# the left side columns
pcaps1, pcaps2 = np.copy(mcaps1), np.copy(mcaps2)
for xpos in reversed(xlefts):
icol = np.mean(img[:,(xpos-spix/2):(xpos+spix/2)],axis=1)
caps1, caps2 = np.array(strip_find(band, icol, dpix=dpix, margin=10))
#print xpos, n_ap, len(caps1), len(caps2)
# check the aperture number based on mcap positions
for i, pcap1, pcap2 in zip(range(n_ap), pcaps1, pcaps2):
tcap1 = caps1[(caps1 < pcap1+ap_thres) & ( caps1 > pcap1-ap_thres)]
if len(tcap1) == 1:
# save this position to the (x, y) position list
apx1[i].append(xpos)
apy1[i].append(tcap1[0])
# save this position for the next tracing loop
pcaps1[i] = tcap1[0]
elif len(tcap1) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap1))
tcap2 = caps2[(caps2 < pcap2+ap_thres) & ( caps2 > pcap2-ap_thres)]
if len(tcap2) == 1:
# save this position to the (x, y) position list
apx2[i].append(xpos)
apy2[i].append(tcap2[0])
# save this position for the next tracing loop
pcaps2[i] = tcap2[0]
elif len(tcap2) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap2))
# the right side columns
pcaps1, pcaps2 = np.copy(mcaps1), np.copy(mcaps2)
for xpos in xrights:
icol = np.mean(img[:,(xpos-spix/2):(xpos+spix/2)],axis=1)
caps1, caps2 = np.array(strip_find(band, icol, dpix=dpix))
print xpos, n_ap, len(caps1), len(caps2)
# check the aperture number based on mcap positions
for i, pcap1, pcap2 in zip(range(n_ap), pcaps1, pcaps2):
tcap1 = caps1[(caps1 < pcap1+ap_thres) & ( caps1 > pcap1-ap_thres)]
if len(tcap1) == 1:
# save this position to the (x, y) position list
apx1[i].append(xpos)
apy1[i].append(tcap1[0])
# save this position for the next tracing loop
pcaps1[i] = tcap1[0]
elif len(tcap1) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap1))
tcap2 = caps2[(caps2 < pcap2+ap_thres) & ( caps2 > pcap2-ap_thres)]
if len(tcap2) == 1:
# save this position to the (x, y) position list
apx2[i].append(xpos)
apy2[i].append(tcap2[0])
# save this position for the next tracing loop
pcaps2[i] = tcap2[0]
elif len(tcap2) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap2))
# sorting the (x, y) positions along x-direction for each aperture
# polynomial fitting with degree
ap_coeffs1, ap_coeffs2 = [], []
z1, z2 = ip.zscale(img)
plt.figure(figsize=(15,15))
plt.imshow(img, cmap='gray', vmin=z1, vmax=z2)
for k in range(len(apx1)): #n_ap):
tapx1 = np.array(apx1[k],dtype=np.float)
tapx2 = np.array(apx2[k],dtype=np.float)
tapy1 = np.array(apy1[k],dtype=np.float)
tapy2 = np.array(apy2[k],dtype=np.float)
tsort1 = np.argsort(tapx1)
tsort2 = np.argsort(tapx2)
coeff1 = np.polynomial.polynomial.polyfit(tapx1[tsort1],tapy1[tsort1],degree)
coeff2 = np.polynomial.polynomial.polyfit(tapx2[tsort2],tapy2[tsort2],degree)
# save the fitting coefficients
ap_coeff = np.zeros([2,degree+1])
ap_coeff[0,:] = coeff1
ap_coeff[1,:] = coeff2
np.savetxt(target_path+'apmap_%s_%02d.%03d.dat' % (band, degree, k), ap_coeff)
ap_coeffs1.append(coeff1)
ap_coeffs2.append(coeff2)
yfit1 = np.polynomial.polynomial.polyval(tapx1[tsort1],coeff1)
yfit2 = np.polynomial.polynomial.polyval(tapx2[tsort2],coeff2)
plt.plot(tapx1[tsort1],tapy1[tsort1], 'go')
plt.plot(tapx2[tsort2],tapy2[tsort2], 'ro')
print 'ap[%d]: delta_y1 = %12.8f %12.8f ' \
% (k, np.mean(tapy1[tsort1]-yfit1), np.std(tapy1[tsort1]-yfit1))
print 'ap[%d]: delta_y2 = %12.8f %12.8f ' \
% (k, np.mean(tapy2[tsort2]-yfit2), np.std(tapy2[tsort2]-yfit2))
xx = np.arange(nx)
yfit1 = np.polynomial.polynomial.polyval(xx,coeff1)
yfit2 = np.polynomial.polynomial.polyval(xx,coeff2)
plt.plot(xx,yfit1,'g-', linewidth=3, alpha=0.6)
plt.plot(xx,yfit2,'r-', linewidth=3, alpha=0.6)
plt.xlim(0,nx)
plt.ylim(0,ny)
plt.show()
plt.savefig(target_path+name+'_aptracing2.png')
plt.close('all')
return ap_coeffs1, ap_coeffs2
def ap_tracing_peak(img, npoints=40, spix=10, dpix=20, thres=1400, \
start_col=None, ap_thres=None, degree=None):
'''
Trace the apertures starting at "start_col" position (for stellar spectrum)
- inputs
1. npoints : slicing number along the column direction
2. spix : summing pixel size along column for finding peaks
3. dpix : detecting pixel range of feature to be regarded as the same
4. thres : detecting intensity level for emission features
5. start_col : starting column number for tracing
6. ap_thres : threshold of pixel range to identify nearby aperture features
7. degree : degree of polynomial fitting
- outputs
coefficients of polynomial fittings for each aperture
'''
# image size
ny, nx = img.shape
# define the threshold pixel range to be matched with nearby aperture positions
if ap_thres == None: ap_thres= nx/npoints/2
# define the degree of polynomials for fitting
if degree == None: degree = 3 #5
# find the apertures in the middle column
if start_col == None: start_col = nx/2
icol = np.mean(img[:,(start_col-spix/2):(start_col+spix/2)],axis=1)
mcaps = peak_find(icol, thres=thres, dpix=dpix)
n_ap = len(mcaps)
# make set of (x, y) positions for each aperture
# add the (x, y) positions at default column
apx = []
apy = []
for mcap in mcaps:
apx.append([start_col])
apy.append([mcap])
# define the tracing direction (left, right)
xsteps = np.linspace(spix,nx-spix,npoints)
xlefts = xsteps[(xsteps < start_col)]
xrights = xsteps[(xsteps > start_col)]
# the left side columns
pcaps = np.copy(mcaps)
for xpos in reversed(xlefts):
icol = np.mean(img[:,(xpos-spix/2):(xpos+spix/2)],axis=1)
caps = np.array(peak_find(icol, dpix=dpix, thres=thres))
print xpos, len(caps), n_ap
# check the aperture number based on mcap positions
for i, pcap in enumerate(pcaps):
tcap = caps[(caps < pcap+ap_thres) & ( caps > pcap-ap_thres)]
if len(tcap) == 1:
# save this position to the (x, y) position list
apx[i].append(xpos)
apy[i].append(tcap[0])
# save this position for the next tracing loop
pcaps[i] = tcap[0]
elif len(tcap) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap))
# the right side columns
pcaps = np.copy(mcaps)
for xpos in xrights:
icol = np.mean(img[:,(xpos-spix/2):(xpos+spix/2)],axis=1)
caps = np.array(peak_find(icol, dpix=dpix, thres=thres))
print xpos, len(caps), n_ap
# check the aperture number based on mcap positions
for i, pcap in enumerate(pcaps):
tcap = caps[(caps < pcap+ap_thres) & ( caps > pcap-ap_thres)]
if len(tcap) == 1:
# save this position to the (x, y) position list
apx[i].append(xpos)
apy[i].append(tcap[0])
# save this position for the next tracing loop
pcaps[i] = tcap[0]
elif len(tcap) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap))
# sorting the (x, y) positions along x-direction for each aperture
# polynomial fitting with degree
ap_coeffs = []
z1, z2 = ip.zscale(img)
plt.imshow(img, cmap='hot', vmin=z1, vmax=z2)
for i in range(n_ap-1):
tapx = np.array(apx[i],dtype=np.float)
tapy = np.array(apy[i],dtype=np.float)
tsort = np.argsort(tapx)
coeff = np.polynomial.polynomial.polyfit(tapx[tsort],tapy[tsort],degree)
ap_coeffs.append(coeff)
yfit = np.polynomial.polynomial.polyval(tapx[tsort],coeff)
plt.plot(tapx[tsort],tapy[tsort], 'go')
plt.plot(tapx[tsort],yfit,'b-', linewidth=10, alpha=0.3)
print 'ap[%d]: delta_y = %12.8f %12.8f ' \
% (i, np.mean(tapy[tsort]-yfit), np.std(tapy[tsort]-yfit))
plt.xlim(0,2048)
plt.ylim(0,2048)
#plt.show()
return ap_coeffs
def _line_identify_old(stripfile, linefile=None, \
npoints=30, spix=4, dpix=5, thres=13000, fdeg=5, desc=''):
def key_press(event):
if event.key == 'q': plt.close('all')
if event.key == 'a':
line_idx = np.argmin((event.xdata - ysignal)**2)
line_x = ysignal[line_idx]
print line_idx, line_x
# mark the points for fitting
ll, = np.where((xx < line_x + dpix) & (xx > line_x - dpix))
print len(ll)
l1 = ax.plot([line_x, line_x], [0, ny],
'r-',
linewidth=5,
alpha=0.5)
l2 = ax.plot(xx[ll], yy[ll], 'ro')
coeff = np.polynomial.polynomial.polyfit(xx[ll], yy[ll], fdeg)
fig.canvas.draw()
print coeff
ycoeff[line_idx, :] = np.array(coeff)
# redraw for the marked points
# read the wavelength for this line
input = raw_input('input wavelength:')
try:
line_wv = np.float(input)
except:
line_wv = 0.0
print line_idx, line_x, line_wv
ywave[line_idx] = line_wv
strip, hdr = ip.readfits(stripfile)
ny, nx = strip.shape
z1, z2 = ip.zscale(strip)
# fitting the base level
snr = 10
ysum = np.average(strip[(ny / 2 - spix):(ny / 2 + spix), :], axis=0)
ll = np.arange(nx)
nrejt = 0
while (1):
yc = np.polynomial.polynomial.polyfit(ll, ysum[ll], fdeg)
yfit = np.polynomial.polynomial.polyval(np.arange(nx), yc)
ll, = np.where(ysum < yfit * (1.0 + 1.0 / snr))
#print nrejt
if nrejt == len(ll): break
nrejt = len(ll)
ysignal = np.array(peak_find(ysum, thres=thres, dpix=dpix))
# define figure object
fig = plt.figure(figsize=(14, 4))
ax = fig.add_subplot(111)
# draw the strip image
ax.imshow(strip, cmap='gray', vmin=z1, vmax=z2, aspect='auto')
ax.set_xlim(0, nx)
ax.set_ylim(-5, ny + 5)
# mark the number of lines
for i, ypeak in enumerate(ysignal):
if i % 2 == 1:
ytext = ny
else:
ytext = -5
ax.text(ypeak, ytext, i + 1, fontsize=15)
# find the emission feature in each row
ysteps = np.linspace(spix, ny - spix, npoints)
# make the array for emission feature points
xx, yy = ([], [])
for ypos in ysteps:
irow = np.mean(strip[(ypos - spix / 2):(ypos + spix / 2), :], axis=0)
#a2.plot(irow)
# find the peak positions
xpos_list = peak_find(irow, dpix=dpix, thres=thres)
# draw and save the peak positions (x, y)
for xpos in xpos_list:
ax.plot(xpos, ypos, 'go', markersize=5, alpha=0.5)
xx.append(xpos)
yy.append(ypos)
# convert into the numpy array
xx = np.array(xx, dtype=np.float)
yy = np.array(yy, dtype=np.float)
# generate the wavelength array for each line
ywave = np.zeros(len(ysignal))
ycoeff = np.zeros([len(ysignal), fdeg + 1])
fig.canvas.mpl_connect('key_press_event', key_press)
print '[a] add line and input wavelength'
print '[r] reset'
print '[q] quit from this aperture'
plt.show()
print 'thanks'
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 ap_tracing_strip(band, filename, npoints=40, spix=10, dpix=20, thres=14000, \
start_col=None, ap_thres=None, degree=None, \
devide=8.0, target_path=MANUAL_PATH):
'''
Trace the apertures starting at "start_col" position (for FLAT spectrum)
- inputs
0. band
1. npoints : slicing number along the column direction
2. spix : summing pixel size along vertical column for finding strips
3. dpix : detecting pixel range of feature to be regarded as the same
4. thres : detecting intensity level for emission features
5. start_col : starting column number for tracing
6. ap_thres : threshold of pixel range to identify nearby aperture features
7. degree : degree of polynomial fitting
- outputs
1. coefficients of polynomial fittings
for start position of each aperture on y-axis
2. coefficients of polynomial fittings
for end position of each aperture on y-axis
'''
img, hdr = ip.readfits(filename)
img, hdr = ip.readfits(filename)
fpath, fname = ip.split_path(filename)
if ip.exist_path(target_path) == False: target_path = fpath
name = '.'.join(fname.split('.')[:-1])
# image size
ny, nx = img.shape
# define the threshold pixel range to be matched with nearby aperture positions
if ap_thres == None: ap_thres = nx / npoints / 4
# define the degree of polynomials for fitting
if degree == None: degree = 3 #7
# find the apertures in the middle column
#if start_col == None: start_col = start_col #1500 #nx/2
icol = np.mean(img[:, (start_col - spix / 2):(start_col + spix / 2)],
axis=1)
#print 'icol', icol, len(icol)
mcaps1, mcaps2 = strip_find(band, icol)
n_ap = len(mcaps1)
# make set of (x, y) positions for each aperture
# add the (x, y) positions at default column
apx1, apx2 = [], []
apy1, apy2 = [], []
for mcap1, mcap2 in zip(mcaps1, mcaps2):
apx1.append([start_col])
apx2.append([start_col])
apy1.append([mcap1])
apy2.append([mcap2])
# define the tracing direction (left, right)
xsteps = np.linspace(spix, nx - spix, npoints)
xlefts = xsteps[(xsteps < start_col)]
xrights = xsteps[(xsteps > start_col)]
# the left side columns
pcaps1, pcaps2 = np.copy(mcaps1), np.copy(mcaps2)
for xpos in reversed(xlefts):
icol = np.mean(img[:, (xpos - spix / 2):(xpos + spix / 2)], axis=1)
caps1, caps2 = np.array(strip_find(band, icol, dpix=dpix, margin=10))
#print xpos, n_ap, len(caps1), len(caps2)
# check the aperture number based on mcap positions
for i, pcap1, pcap2 in zip(range(n_ap), pcaps1, pcaps2):
tcap1 = caps1[(caps1 < pcap1 + ap_thres)
& (caps1 > pcap1 - ap_thres)]
if len(tcap1) == 1:
# save this position to the (x, y) position list
apx1[i].append(xpos)
apy1[i].append(tcap1[0])
# save this position for the next tracing loop
pcaps1[i] = tcap1[0]
elif len(tcap1) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap1))
tcap2 = caps2[(caps2 < pcap2 + ap_thres)
& (caps2 > pcap2 - ap_thres)]
if len(tcap2) == 1:
# save this position to the (x, y) position list
apx2[i].append(xpos)
apy2[i].append(tcap2[0])
# save this position for the next tracing loop
pcaps2[i] = tcap2[0]
elif len(tcap2) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap2))
# the right side columns
pcaps1, pcaps2 = np.copy(mcaps1), np.copy(mcaps2)
for xpos in xrights:
icol = np.mean(img[:, (xpos - spix / 2):(xpos + spix / 2)], axis=1)
caps1, caps2 = np.array(strip_find(band, icol, dpix=dpix))
print xpos, n_ap, len(caps1), len(caps2)
# check the aperture number based on mcap positions
for i, pcap1, pcap2 in zip(range(n_ap), pcaps1, pcaps2):
tcap1 = caps1[(caps1 < pcap1 + ap_thres)
& (caps1 > pcap1 - ap_thres)]
if len(tcap1) == 1:
# save this position to the (x, y) position list
apx1[i].append(xpos)
apy1[i].append(tcap1[0])
# save this position for the next tracing loop
pcaps1[i] = tcap1[0]
elif len(tcap1) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap1))
tcap2 = caps2[(caps2 < pcap2 + ap_thres)
& (caps2 > pcap2 - ap_thres)]
if len(tcap2) == 1:
# save this position to the (x, y) position list
apx2[i].append(xpos)
apy2[i].append(tcap2[0])
# save this position for the next tracing loop
pcaps2[i] = tcap2[0]
elif len(tcap2) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap2))
# sorting the (x, y) positions along x-direction for each aperture
# polynomial fitting with degree
ap_coeffs1, ap_coeffs2 = [], []
z1, z2 = ip.zscale(img)
plt.figure(figsize=(15, 15))
plt.imshow(img, cmap='gray', vmin=z1, vmax=z2)
for k in range(len(apx1)): #n_ap):
tapx1 = np.array(apx1[k], dtype=np.float)
tapx2 = np.array(apx2[k], dtype=np.float)
tapy1 = np.array(apy1[k], dtype=np.float)
tapy2 = np.array(apy2[k], dtype=np.float)
tsort1 = np.argsort(tapx1)
tsort2 = np.argsort(tapx2)
coeff1 = np.polynomial.polynomial.polyfit(tapx1[tsort1], tapy1[tsort1],
degree)
coeff2 = np.polynomial.polynomial.polyfit(tapx2[tsort2], tapy2[tsort2],
degree)
# save the fitting coefficients
ap_coeff = np.zeros([2, degree + 1])
ap_coeff[0, :] = coeff1
ap_coeff[1, :] = coeff2
np.savetxt(target_path + 'apmap_%s_%02d.%03d.dat' % (band, degree, k),
ap_coeff)
ap_coeffs1.append(coeff1)
ap_coeffs2.append(coeff2)
yfit1 = np.polynomial.polynomial.polyval(tapx1[tsort1], coeff1)
yfit2 = np.polynomial.polynomial.polyval(tapx2[tsort2], coeff2)
plt.plot(tapx1[tsort1], tapy1[tsort1], 'go')
plt.plot(tapx2[tsort2], tapy2[tsort2], 'ro')
print 'ap[%d]: delta_y1 = %12.8f %12.8f ' \
% (k, np.mean(tapy1[tsort1]-yfit1), np.std(tapy1[tsort1]-yfit1))
print 'ap[%d]: delta_y2 = %12.8f %12.8f ' \
% (k, np.mean(tapy2[tsort2]-yfit2), np.std(tapy2[tsort2]-yfit2))
xx = np.arange(nx)
yfit1 = np.polynomial.polynomial.polyval(xx, coeff1)
yfit2 = np.polynomial.polynomial.polyval(xx, coeff2)
plt.plot(xx, yfit1, 'g-', linewidth=3, alpha=0.6)
plt.plot(xx, yfit2, 'r-', linewidth=3, alpha=0.6)
plt.xlim(0, nx)
plt.ylim(0, ny)
plt.show()
plt.savefig(target_path + name + '_aptracing2.png')
plt.close('all')
return ap_coeffs1, ap_coeffs2
def ap_tracing_peak(img, npoints=40, spix=10, dpix=20, thres=1400, \
start_col=None, ap_thres=None, degree=None):
'''
Trace the apertures starting at "start_col" position (for stellar spectrum)
- inputs
1. npoints : slicing number along the column direction
2. spix : summing pixel size along column for finding peaks
3. dpix : detecting pixel range of feature to be regarded as the same
4. thres : detecting intensity level for emission features
5. start_col : starting column number for tracing
6. ap_thres : threshold of pixel range to identify nearby aperture features
7. degree : degree of polynomial fitting
- outputs
coefficients of polynomial fittings for each aperture
'''
# image size
ny, nx = img.shape
# define the threshold pixel range to be matched with nearby aperture positions
if ap_thres == None: ap_thres = nx / npoints / 2
# define the degree of polynomials for fitting
if degree == None: degree = 3 #5
# find the apertures in the middle column
if start_col == None: start_col = nx / 2
icol = np.mean(img[:, (start_col - spix / 2):(start_col + spix / 2)],
axis=1)
mcaps = peak_find(icol, thres=thres, dpix=dpix)
n_ap = len(mcaps)
# make set of (x, y) positions for each aperture
# add the (x, y) positions at default column
apx = []
apy = []
for mcap in mcaps:
apx.append([start_col])
apy.append([mcap])
# define the tracing direction (left, right)
xsteps = np.linspace(spix, nx - spix, npoints)
xlefts = xsteps[(xsteps < start_col)]
xrights = xsteps[(xsteps > start_col)]
# the left side columns
pcaps = np.copy(mcaps)
for xpos in reversed(xlefts):
icol = np.mean(img[:, (xpos - spix / 2):(xpos + spix / 2)], axis=1)
caps = np.array(peak_find(icol, dpix=dpix, thres=thres))
print xpos, len(caps), n_ap
# check the aperture number based on mcap positions
for i, pcap in enumerate(pcaps):
tcap = caps[(caps < pcap + ap_thres) & (caps > pcap - ap_thres)]
if len(tcap) == 1:
# save this position to the (x, y) position list
apx[i].append(xpos)
apy[i].append(tcap[0])
# save this position for the next tracing loop
pcaps[i] = tcap[0]
elif len(tcap) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap))
# the right side columns
pcaps = np.copy(mcaps)
for xpos in xrights:
icol = np.mean(img[:, (xpos - spix / 2):(xpos + spix / 2)], axis=1)
caps = np.array(peak_find(icol, dpix=dpix, thres=thres))
print xpos, len(caps), n_ap
# check the aperture number based on mcap positions
for i, pcap in enumerate(pcaps):
tcap = caps[(caps < pcap + ap_thres) & (caps > pcap - ap_thres)]
if len(tcap) == 1:
# save this position to the (x, y) position list
apx[i].append(xpos)
apy[i].append(tcap[0])
# save this position for the next tracing loop
pcaps[i] = tcap[0]
elif len(tcap) == 0:
print 'ap[%d](x=%d) : The matching aperture position was not found' \
% (i, xpos)
else:
print 'ap[%d](x=%d) : The matching aperture position was too many(%d)' \
% (i, xpos, len(tcap))
# sorting the (x, y) positions along x-direction for each aperture
# polynomial fitting with degree
ap_coeffs = []
z1, z2 = ip.zscale(img)
plt.imshow(img, cmap='hot', vmin=z1, vmax=z2)
for i in range(n_ap - 1):
tapx = np.array(apx[i], dtype=np.float)
tapy = np.array(apy[i], dtype=np.float)
tsort = np.argsort(tapx)
coeff = np.polynomial.polynomial.polyfit(tapx[tsort], tapy[tsort],
degree)
ap_coeffs.append(coeff)
yfit = np.polynomial.polynomial.polyval(tapx[tsort], coeff)
plt.plot(tapx[tsort], tapy[tsort], 'go')
plt.plot(tapx[tsort], yfit, 'b-', linewidth=10, alpha=0.3)
print 'ap[%d]: delta_y = %12.8f %12.8f ' \
% (i, np.mean(tapy[tsort]-yfit), np.std(tapy[tsort]-yfit))
plt.xlim(0, 2048)
plt.ylim(0, 2048)
#plt.show()
return ap_coeffs
def check(stripfile, aperture, tstrip, lxx_t, lwave, b, linear_wave, pngpath='', datpath='', outputname=''):
# Input images
img, ahdr = ip.readfits(stripfile)
ny, nx = img.shape
wavel = np.array(lwave)
npix = 9 # Range pixel of each identify lines
# The belove steps are used to check the transform processes.
ti_peakline, tlwidth = peak_reidentify(tstrip, npix, lxx_t)
npix = np.zeros(len(lxx_t))
for i in range(len(lxx_t)):
npix[i] = round(np.average(tlwidth[i]))*2 + 1
tilxx = np.zeros(len(lxx_t))
for i in range(len(lxx_t)):
tilxx[i] = ti_peakline[i][2]
#print 'identify lxx', tilxx
peak_w = reidentify(tstrip, npix, list(tilxx))
# Check peak line stable of Gaussian profile
for i in range(len(peak_w)):
for j in range(len(peak_w[i])):
if (peak_w[i][j] - np.median(peak_w[i])) > 3:
peak_w[i][j] = np.median(peak_w[i])
if (peak_w[i][j] - np.median(peak_w[i])) < -3:
peak_w[i][j] = np.median(peak_w[i])
# Using polynomial to fit the emission lines
tfit_x, tvmiddle = linefitting(tstrip, peak_w, lxx_t)
# Test distortion of emission lines
residual(peak_w, tvmiddle)
# txx values transform
step = int(ny/6)
txx = np.zeros(len(lxx_t))
for i in range(0, len(lxx_t)):
txx[i] = peak_w[i][2] # Sum of 10 lines in the middle stripfile
#print 'center of identify lines after transform', txx
# Second order
coeff2 = np.polynomial.polynomial.polyfit(wavel, txx, 2)
#print 'cofficient fitting linear wave', coeff2
tp_min = [coeff2[2], coeff2[1], coeff2[0]]
tvalue_min = np.roots(tp_min)
tp_max = [coeff2[2], coeff2[1], coeff2[0] - 2047]
tvalue_max = np.roots(tp_max)
tlamda_min = find_nearest(tvalue_min, min(wavel))
tlamda_max = find_nearest(tvalue_max, max(wavel))
#print 'position', np.where(tvalue_min == tlamda_min)[0], np.where(tvalue_max == tlamda_max)[0]
#print 'lambda min and max', tlamda_min, tlamda_max
# Position array
position = np.where(tvalue_max == tlamda_max)[0]
# Check in case of complex values
if (np.iscomplexobj(tlamda_min)):
lamda_min = np.real(tlamda_min)
elif (np.iscomplexobj(tlamda_max)):
lamda_max = np.real(tlamda_max)
tlamda = np.zeros(nx)
for i in range(nx):
pt = [coeff2[2], coeff2[1], coeff2[0] - i]
if (np.iscomplexobj(np.roots(pt))):
temp = np.real(np.roots(pt))
tlamda[i] = temp[position]
else:
tlamda[i] = np.roots(pt)[position]
# 4nd order
'''
coeff2 = np.polynomial.polynomial.polyfit(wavel, txx, 4)
print 'cofficient fitting linear wave', coeff2
tp_min = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0]]
tvalue_min = np.roots(tp_min)
tp_max = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0] - 2047]
tvalue_max = np.roots(tp_max)
tlamda_min = find_nearest(tvalue_min, min(wavel))
tlamda_max = find_nearest(tvalue_max, max(wavel))
print 'position', np.where(tvalue_min == tlamda_min)[0], np.where(tvalue_max == tlamda_max)[0]
print 'lambda min and max', tlamda_min, tlamda_max
print 'lambda min and max after transform', tlamda_min, tlamda_max
tlamda = np.zeros(nx)
for i in range(nx):
p = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0] - i]
tlamda[i] = np.roots(p)[np.where(tvalue_min == tlamda_min)[0]]
'''
#fig = plt.figure(4, figsize=(10,8))
#a = fig.add_subplot(111)
#a.plot(tlamda, range(nx), 'r', wavel, txx, 'ko')
#a.plot(wavel, txx, 'ko')
#plt.ylabel('X-position [pixels]')
#plt.xlabel('Wavelength [microns]')
#plt.legend(['Polyfit', 'X-after transform'])
#plt.show()
# Test file of results
# wavelength calculate from the linear equation from the
# line lists
f_linear = np.zeros(len(wavel))
for i in range(len(wavel)):
f_linear[i] = b[0] + b[1] * wavel[i]
#print 'linear coeff', b
f = open(datpath + outputname + str(aperture) + '.dat','w')
A = np.arange(len(f_linear))
for j in range(len(peak_w[0])):
for i in A:
temp = "%.6f %.6f %.6f %.6f \n" %(wavel[i], f_linear[i], np.array(peak_w[i][j]), \
np.array(peak_w[i][j]) - f_linear[i])
f.write(temp)
f.close()
# Draw the strip image
f6 = plt.figure(None, figsize=(14,6))
ax6= f6.add_subplot(311, title= outputname + str(aperture))
z1, z2 = ip.zscale(tstrip)
ax6.imshow(img, cmap='hot',vmin=z1, vmax=z2, aspect='auto')
ax6.set_xlim(0,nx)
ax6.set_ylim(-10,ny+10)
plt.ylabel('Y [pixels]')
#plt.xlabel('X [pixels]')
#f7 = plt.figure(7, figsize=(14,3))
ax7= f6.add_subplot(312)
ax7.imshow(tstrip, cmap='hot',vmin=z1, vmax=z2, aspect='auto')
#ax7.plot(range(nx), img_shift[ny/2,:], 'k.', trxx, tstrip[ny/2,:], 'r.')
#plt.legend(['before transform', 'after transform'])
ax7.set_xlim(0,nx)
ax7.set_ylim(-10,ny+10)
#plt.xlabel('X [pixels]')
#f8 = plt.figure(8, figsize=(14,3))
ax8 = f6.add_subplot(313, title='')
ax8.plot(linear_wave, tstrip[ny/2,:], 'b')
#ax4.set_xlim(0, len(tstrip[1,:]))
#ax4.set_ylim(-10,ny+10)
#ax4.set_xlim(min(w_fitting), max(w_fitting))
ax8.set_xlim(min(linear_wave), max(linear_wave))
plt.xlabel('Wavelength [microns]')
plt.savefig(pngpath + outputname + str(aperture) + '.png')
plt.close()
return coeff2
def draw_strips(strip, wave, desc='', linedata=[], lampname='', grayplot=False, \
target_path=PNG_PATH):
'''
Draw the strips with wavelength
- INPUTS:
1. strip data
2. wavelength data
3. line data
- OUTPUTS:
PNG files
'''
#print 'draw_strips', lampname
if len(linedata) > 0:
cwv, cflx = linedata
wmin, wmax = (np.min(wave), np.max(wave))
z1, z2 = ip.zscale(strip)
f2 = plt.figure(2, figsize=(12, 5), dpi=200)
a1 = f2.add_subplot(211, aspect='auto')
a2 = f2.add_subplot(212, aspect='auto')
ny, nx = strip.shape
cuty = ny / 2 - 8
a1.imshow(strip, cmap='hot', aspect=nx / 1000.0, vmin=z1, vmax=z2)
a1.plot([0, nx], [cuty, cuty], 'g--', alpha=0.8, linewidth=3)
a1.set_xlim((0, nx))
a1.set_ylim((0, ny))
a1.set_title('%s' % (desc, ))
a2.plot(wave, strip[cuty, :], 'b-', linewidth=1)
ww = np.where((cwv < wmax) & (cwv > wmin))[0]
fmax = np.zeros([len(ww)]) + np.max(strip[cuty, :]) * 1.05
a2.plot(cwv[ww], fmax, 'r|', markersize=10, markeredgewidth=2, alpha=0.7)
if lampname != '': lampname = '(' + lampname + ')'
a2.set_title('%s %s' % (desc, lampname))
a2.set_xlabel('Wavelength [um]')
a2.set_xlim((wmin, wmax))
a2.set_ylim((0, fmax[0] * 1.1))
# f2.savefig(target_path+'%s_prof.png' % (desc,)) #2013-11-21 cksim commented this
f2.savefig(target_path + '%s.png' % (desc, )) #2013-11-21 cksim
if grayplot == True:
f3 = plt.figure(3, figsize=(12, 5), dpi=200)
a3 = f3.add_subplot(111)
a3.imshow(strip, cmap='gray', aspect=nx / 200.0, vmin=z1, vmax=z2)
x, y = (np.arange(nx), np.sum(strip, axis=0))
a3.plot(x, (y-np.min(y))/(np.max(y)-np.min(y))*ny*0.9,\
'b-', linewidth=3, alpha=0.7)
x, y = ((cwv[ww] - wmin) / (wmax - wmin) * (nx - 1),
np.zeros(len(ww)) + ny * 1.05)
a3.plot(x, y, 'r|', markersize=10, markeredgewidth=2, alpha=0.7)
a3.set_xlim((0, nx))
a3.set_ylim((0, ny * 1.1))
cticks = wticks[np.where((wticks > wmin) & (wticks < wmax))]
xticks = (cticks - wmin) / (wmax - wmin) * (nx - 1)
#print xticks
a3.set_yticks([])
a3.set_xticks(xticks)
a3.set_xticklabels(['%.3f' % x for x in cticks])
a3.set_xlabel('Wavelength [um]')
f3.savefig(target_path + '%s_gray.png' % (desc, ))
plt.close('all')
def check(stripfile,
aperture,
tstrip,
lxx_t,
lwave,
b,
linear_wave,
pngpath='',
datpath='',
outputname=''):
# Input images
img, ahdr = ip.readfits(stripfile)
ny, nx = img.shape
wavel = np.array(lwave)
npix = 9 # Range pixel of each identify lines
# The belove steps are used to check the transform processes.
ti_peakline, tlwidth = peak_reidentify(tstrip, npix, lxx_t)
npix = np.zeros(len(lxx_t))
for i in range(len(lxx_t)):
npix[i] = round(np.average(tlwidth[i])) * 2 + 1
tilxx = np.zeros(len(lxx_t))
for i in range(len(lxx_t)):
tilxx[i] = ti_peakline[i][2]
#print 'identify lxx', tilxx
peak_w = reidentify(tstrip, npix, list(tilxx))
# Check peak line stable of Gaussian profile
for i in range(len(peak_w)):
for j in range(len(peak_w[i])):
if (peak_w[i][j] - np.median(peak_w[i])) > 3:
peak_w[i][j] = np.median(peak_w[i])
if (peak_w[i][j] - np.median(peak_w[i])) < -3:
peak_w[i][j] = np.median(peak_w[i])
# Using polynomial to fit the emission lines
tfit_x, tvmiddle = linefitting(tstrip, peak_w, lxx_t)
# Test distortion of emission lines
residual(peak_w, tvmiddle)
# txx values transform
step = int(ny / 6)
txx = np.zeros(len(lxx_t))
for i in range(0, len(lxx_t)):
txx[i] = peak_w[i][2] # Sum of 10 lines in the middle stripfile
#print 'center of identify lines after transform', txx
# Second order
coeff2 = np.polynomial.polynomial.polyfit(wavel, txx, 2)
#print 'cofficient fitting linear wave', coeff2
tp_min = [coeff2[2], coeff2[1], coeff2[0]]
tvalue_min = np.roots(tp_min)
tp_max = [coeff2[2], coeff2[1], coeff2[0] - 2047]
tvalue_max = np.roots(tp_max)
tlamda_min = find_nearest(tvalue_min, min(wavel))
tlamda_max = find_nearest(tvalue_max, max(wavel))
#print 'position', np.where(tvalue_min == tlamda_min)[0], np.where(tvalue_max == tlamda_max)[0]
#print 'lambda min and max', tlamda_min, tlamda_max
# Position array
position = np.where(tvalue_max == tlamda_max)[0]
# Check in case of complex values
if (np.iscomplexobj(tlamda_min)):
lamda_min = np.real(tlamda_min)
elif (np.iscomplexobj(tlamda_max)):
lamda_max = np.real(tlamda_max)
tlamda = np.zeros(nx)
for i in range(nx):
pt = [coeff2[2], coeff2[1], coeff2[0] - i]
if (np.iscomplexobj(np.roots(pt))):
temp = np.real(np.roots(pt))
tlamda[i] = temp[position]
else:
tlamda[i] = np.roots(pt)[position]
# 4nd order
'''
coeff2 = np.polynomial.polynomial.polyfit(wavel, txx, 4)
print 'cofficient fitting linear wave', coeff2
tp_min = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0]]
tvalue_min = np.roots(tp_min)
tp_max = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0] - 2047]
tvalue_max = np.roots(tp_max)
tlamda_min = find_nearest(tvalue_min, min(wavel))
tlamda_max = find_nearest(tvalue_max, max(wavel))
print 'position', np.where(tvalue_min == tlamda_min)[0], np.where(tvalue_max == tlamda_max)[0]
print 'lambda min and max', tlamda_min, tlamda_max
print 'lambda min and max after transform', tlamda_min, tlamda_max
tlamda = np.zeros(nx)
for i in range(nx):
p = [coeff2[4], coeff2[3], coeff2[2], coeff2[1], coeff2[0] - i]
tlamda[i] = np.roots(p)[np.where(tvalue_min == tlamda_min)[0]]
'''
#fig = plt.figure(4, figsize=(10,8))
#a = fig.add_subplot(111)
#a.plot(tlamda, range(nx), 'r', wavel, txx, 'ko')
#a.plot(wavel, txx, 'ko')
#plt.ylabel('X-position [pixels]')
#plt.xlabel('Wavelength [microns]')
#plt.legend(['Polyfit', 'X-after transform'])
#plt.show()
# Test file of results
# wavelength calculate from the linear equation from the
# line lists
f_linear = np.zeros(len(wavel))
for i in range(len(wavel)):
f_linear[i] = b[0] + b[1] * wavel[i]
#print 'linear coeff', b
f = open(datpath + outputname + str(aperture) + '.dat', 'w')
A = np.arange(len(f_linear))
for j in range(len(peak_w[0])):
for i in A:
temp = "%.6f %.6f %.6f %.6f \n" %(wavel[i], f_linear[i], np.array(peak_w[i][j]), \
np.array(peak_w[i][j]) - f_linear[i])
f.write(temp)
f.close()
# Draw the strip image
f6 = plt.figure(None, figsize=(14, 6))
ax6 = f6.add_subplot(311, title=outputname + str(aperture))
z1, z2 = ip.zscale(tstrip)
ax6.imshow(img, cmap='hot', vmin=z1, vmax=z2, aspect='auto')
ax6.set_xlim(0, nx)
ax6.set_ylim(-10, ny + 10)
plt.ylabel('Y [pixels]')
#plt.xlabel('X [pixels]')
#f7 = plt.figure(7, figsize=(14,3))
ax7 = f6.add_subplot(312)
ax7.imshow(tstrip, cmap='hot', vmin=z1, vmax=z2, aspect='auto')
#ax7.plot(range(nx), img_shift[ny/2,:], 'k.', trxx, tstrip[ny/2,:], 'r.')
#plt.legend(['before transform', 'after transform'])
ax7.set_xlim(0, nx)
ax7.set_ylim(-10, ny + 10)
#plt.xlabel('X [pixels]')
#f8 = plt.figure(8, figsize=(14,3))
ax8 = f6.add_subplot(313, title='')
ax8.plot(linear_wave, tstrip[ny / 2, :], 'b')
#ax4.set_xlim(0, len(tstrip[1,:]))
#ax4.set_ylim(-10,ny+10)
#ax4.set_xlim(min(w_fitting), max(w_fitting))
ax8.set_xlim(min(linear_wave), max(linear_wave))
plt.xlabel('Wavelength [microns]')
plt.savefig(pngpath + outputname + str(aperture) + '.png')
plt.close()
return coeff2