def make_RGB(sigmax=3,sigmin=1,write=False):
Blue,header = fits.getdata('Blue.fit',0,header=True)
Green,header = fits.getdata('Green.fit',0,header=True)
Red,header = fits.getdata('Red.fit',0,header=True)
bmed = np.median(Blue)
gmed = np.median(Green)
rmed = np.median(Red)
bsig = rb.std(Blue)
gsig = rb.std(Green)
rsig = rb.std(Red)
final = np.zeros((Blue.shape[0],Blue.shape[1],3),dtype=float)
final[:,:,0] = img_scale.sqrt(Red,scale_min=rmed+sigmin*rsig,scale_max=rmed+sigmax*rsig)
final[:,:,1] = img_scale.sqrt(Green,scale_min=gmed+sigmin*gsig,scale_max=gmed+sigmax*gsig)
final[:,:,2] = img_scale.sqrt(Blue,scale_min=bmed+sigmin*bsig,scale_max=bmed+sigmax*bsig)
plt.ion()
plt.figure(99)
plt.imshow(final,aspect='equal')
if write:
plt.savefig('RGB.png',dpi=300)
return
def wind_dir_pressure(year=2013):
from statsmodels.nonparametric.kernel_density import KDEMultivariate as KDE
import robust as rb
min2 = 0
sigfac = 3
sigsamp = 5
d = get_data(year=year)
wdir = d["winddir_deg"]
wdir_rand = wdir + np.random.normal(0,12,len(wdir))
bad = np.isnan(wdir_rand)
wdir_rand[bad] = np.random.uniform(0,360,np.sum(bad))
press = d["pressure"]
dist1 = wdir_rand
dist2 = press
med1 = np.median(dist1)
sig1 = rb.std(dist1)
datamin1 = np.min(dist1)
datamax1 = np.max(dist1)
min1 = 0.0
max1 = 360.0
med2 = np.median(dist2)
sig2 = rb.std(dist2)
datamin2 = np.min(dist2)
datamax2 = np.max(dist2)
min2 = np.min(dist2)
max2 = np.max(dist2)
X, Y = np.mgrid[min1:max1:100j, min2:max2:100j]
positions = np.vstack([X.ravel(), Y.ravel()])
values = np.vstack([dist1, dist2])
kernel = KDE(values,var_type='cc',bw=[sig1/sigsamp,sig2/sigsamp])
Z = np.reshape(kernel.pdf(positions).T, X.shape)
aspect = (max1-min1)/(max2-min2) * 8.5/11.0
plot_params()
plt.ion()
plt.figure(5,figsize=(11,8.5))
plt.clf()
ax = plt.subplot(111)
ax.imshow(np.rot90(Z), cmap=plt.cm.CMRmap_r,aspect=aspect, \
extent=[min1, max1, min2, max2],origin='upper')
ax.yaxis.labelpad = 12
ax.set_ylabel('Atmospheric Pressure (in-Hg)',fontsize=fs)
ax.set_xlabel('Wind Direction (degrees)',fontsize=fs)
plt.title('Wind Direction and Pressure at Thacher Observatory in '+str(year),fontsize=fs)
plt.savefig('Wind_Direction_Pressure_'+str(year)+'.png',dpi=300)
mpl.rcdefaults()
return
def make_RGB():
Blue,header = pf.getdata('Blue.fit',0,header=True)
Green,header = pf.getdata('Green.fit',0,header=True)
Red,header = pf.getdata('Red.fit',0,header=True)
G = h.pyfits.open('Green.fit')
Gh = h.pyfits.getheader('Green.fit')
B = h.pyfits.open('Blue.fit')
Bh = h.pyfits.getheader('Blue.fit')
R = h.pyfits.open('Red.fit')
Rh = h.pyfits.getheader('Red.fit')
Bnew = h.hcongrid(B[0].data,B[0].header,Gh)
Rnew = h.hcongrid(R[0].data,R[0].header,Gh)
Blue = Bnew
Green,header = readimage('Green.fit')
Red = Rnew
bmed = np.median(Blue)
gmed = np.median(Green)
rmed = np.median(Red)
bsig = rb.std(Blue)
gsig = rb.std(Green)
rsig = rb.std(Red)
final = np.zeros((Blue.shape[0],Blue.shape[1],3),dtype=float)
sigmin = 1.25
sigmax = 15
final[:,:,0] = img_scale.sqrt(Red,scale_min=rmed+sigmin*rsig,scale_max=rmed+0.6*sigmax*rsig)
final[:,:,1] = img_scale.sqrt(Green,scale_min=gmed+sigmin*gsig,scale_max=gmed+0.6*sigmax*gsig)
final[:,:,2] = img_scale.sqrt(Blue,scale_min=bmed+sigmin*bsig,scale_max=bmed+0.6*sigmax*bsig)
plt.ion()
plt.figure(99)
#plt.imshow(img,aspect='equal')
plt.xlim(250,1550)
plt.ylim(288,1588)
plt.xticks([])
plt.yticks([])
plt.imshow(final,aspect='equal')
return
def show_image(file,lowsig=1,hisig=4,skyonly=False,write=False):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
# Keep region determined by eye
image = image[:,200:1270]
# Region of sky to determine statistics determined by eye
if skyonly:
region = image[280:775,200:900]
else:
region = image
sig = rb.std(region)
med = np.median(region)
mean = np.mean(region)
vmin = med - lowsig*sig
vmax = med + hisig*sig
plt.ion()
plt.figure(99,figsize=(15,8))
plt.clf()
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray',
interpolation='nearest',origin='upper')
plt.axis('off')
plt.colorbar()
if write:
plt.savefig('AllSkyImage.png',dpi=300)
return
def movie_image(file,lowsig=1,hisig=4):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
date = header['DATE-OBS']
time = 'UT'+header['TIME-OBS']
# Keep region determined by eye
image = image[:,200:1270]
# Do statistics for image display
sig = rb.std(image)
med = np.median(image)
mean = np.mean(image)
vmin = med - lowsig*sig
vmax = med + hisig*sig
# Plot image
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray',
interpolation='nearest',origin='upper')
plt.annotate(date,[0.08,0.92],horizontalalignment='left',
xycoords='figure fraction',fontsize=14,color='white')
plt.annotate(time,[0.92,0.92],horizontalalignment='right',
xycoords='figure fraction',fontsize=14,color='white')
# Turn axis labeling off
plt.axis('off')
return
def clip2(data, robust=True):
"""
Alternate sigma-clipping flagger for spectrometer data. This function
assumes that the data have already been bandpassed in frequency and
time and then uses a iterative method to find and flag outliters.
"""
for j in xrange(params.sc_passes):
mask = data.mask * 1
for i in range(data.shape[1]):
i0 = max([0, i - params.sc_bp_window_f / 2])
i1 = min([i + params.sc_bp_window_f / 2, data.shape[1] - 1])
try:
assert (robust)
mn, st = robust.mean(data[:, i0:i1 + 1]), robust.std(
data[:, i0:i1 + 1])
except:
mn, st = np.ma.mean(data[:, i0:i1 + 1]), np.ma.std(
data[:, i0:i1 + 1])
bad = np.where(np.abs(data[:, i] - 1) > params.sigma * st)[0]
mask[bad, i] |= True
data.mask = mask * 1
return data.mask
def show_image(image,siglo=3,sighi=7):
med = np.median(image)
sig = rb.std(image)
plt.ion()
plt.figure()
vmin = med - siglo*sig
vmax = med + sighi*sig
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray')
return
def display_image(image,siglo=3,sighi=7,fignum=2):
med = np.median(image)
sig = rb.std(image)
plt.ion()
plt.figure(fignum)
vmin = med - siglo*sig
vmax = med + sighi*sig
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray')
return
def readimage(imfile,plot=False,siglo=3,sighi=7):
image,header = fits.getdata(imfile,0,header=True)
med = np.median(image)
sig = rb.std(image)
if plot:
plt.ion()
plt.figure(1)
vmin = med - siglo*sig
vmax = med + sighi*sig
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray')
return image,header
def compareData(name1, name2, plot=False):
#read data
data1 = data[data['Name']== name1]['Length']
data2 = data[data['Name']== name2]['Length']
#exclude outliers
mean1, mean2 = rb.mean(data1.values), rb.mean(data2.values)
std1, std2 = rb.std(data1.values), rb.std(data2.values)
data1 = data1[data1.values>(mean1-std1)]
data2 = data2[data2.values>(mean2-std2)]
#std1 = np.std(lengths1)
if plot:
#plot histograms
plt.ion()
plt.figure(1)
plt.clf()
plt.hist(data1.values,bins=np.linspace(4.75,5.75,30),
label=name1, alpha=0.5,histtype='barstacked',stacked=True)
plt.hist(data2.values,bins=np.linspace(4.75,5.75,30),
label=name2, alpha=0.5,histtype='barstacked',stacked=True)
plt.legend()
#plot CDFs
plt.figure(2)
xs1 = np.sort(data1)
ys1 = np.arange(1, len(xs1)+1)/float(len(xs1))
plt.plot(xs1,ys1,'g-',label=name1)
cdf = ECDF(data2)
plt.plot(cdf.x, cdf.y,'r-',label=name2)
plt.legend()
#preform ks test and student t-test
d,pk = ks_2samp(data1,data2)
t,pt = ttest_ind(data1,data2,equal_var=False)
#print d,pk,pt
return pk, pt
def data_look(file,lowsig=1,hisig=4):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
sig = rb.std(image)
med = np.median(image)
mean = np.mean(image)
vmin = med - lowsig*sig
vmax = med + hisig*sig
plt.ion()
plt.figure(99,figsize=(15,8))
plt.clf()
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray',
interpolation='nearest',origin='upper')
plt.axis('off')
plt.colorbar()
def display_image(file,lowsig=1,hisig=4):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
# Do statistics for image display
sig = rb.std(image)
med = np.median(image)
mean = np.mean(image)
vmin = med - lowsig*sig
vmax = med + hisig*sig
# Plot image
plt.imshow(image,vmin=vmin,vmax=vmax,cmap='gray',
interpolation='nearest',origin='upper')
# Turn axis labeling off
plt.axis('off')
return
def data_look(file, lowsig=1, hisig=4):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
sig = rb.std(image)
med = np.median(image)
mean = np.mean(image)
vmin = med - lowsig * sig
vmax = med + hisig * sig
plt.ion()
plt.figure(99, figsize=(15, 8))
plt.clf()
plt.imshow(image,
vmin=vmin,
vmax=vmax,
cmap='gray',
interpolation='nearest',
origin='upper')
plt.axis('off')
plt.colorbar()
def display_image(file, lowsig=1, hisig=4):
# Get image and header
image, header = pf.getdata(file, 0, header=True)
# Do statistics for image display
sig = rb.std(image)
med = np.median(image)
mean = np.mean(image)
vmin = med - lowsig * sig
vmax = med + hisig * sig
# Plot image
plt.imshow(image,
vmin=vmin,
vmax=vmax,
cmap='gray',
interpolation='nearest',
origin='upper')
# Turn axis labeling off
plt.axis('off')
return
def wind_speed_pressure(year=2013,peak=False):
from statsmodels.nonparametric.kernel_density import KDEMultivariate as KDE
import robust as rb
min2 = 0
sigfac = 3
sigsamp = 5
d = get_data(year=year)
if peak:
wind = d['windhi']
tag = 'peak'
word = 'Peak '
else:
wind = d["wind"]
tag = 'ave'
word = 'Average '
wind_rand = wind + np.random.normal(0,0.5,len(wind))
press = d["pressure"]
dist1 = press
dist2 = wind_rand
med1 = np.median(dist1)
sig1 = rb.std(dist1)
datamin1 = np.min(dist1)
datamax1 = np.max(dist1)
min1 = np.min(dist1)
max1 = np.max(dist1)
med2 = np.median(dist2)
sig2 = rb.std(dist2)
datamin2 = np.min(dist2)
datamax2 = np.max(dist2)
max2 = min(med2 + sigfac*sig2,datamax2)
X, Y = np.mgrid[min1:max1:100j, min2:max2:100j]
positions = np.vstack([X.ravel(), Y.ravel()])
values = np.vstack([dist1, dist2])
kernel = KDE(values,var_type='cc',bw=[sig1/sigsamp,sig2/sigsamp])
Z = np.reshape(kernel.pdf(positions).T, X.shape)
aspect = (max1-min1)/(max2-min2) * 8.5/11.0
plot_params()
plt.ion()
plt.figure(5,figsize=(11,8.5))
plt.clf()
ax = plt.subplot(111)
ax.imshow(np.rot90(Z), cmap=plt.cm.CMRmap_r,aspect=aspect, \
extent=[min1, max1, min2, max2],origin='upper')
ax.yaxis.labelpad = 12
ax.set_xlabel('Atmospheric Pressure (in-Hg)',fontsize=fs)
ax.set_ylabel(word+'Wind Speed (mph)',fontsize=fs)
plt.title('Wind Speed and Pressure at Thacher Observatory in '+str(year),fontsize=fs)
plt.savefig('Wind'+tag+'_Pressure_'+str(year)+'.png',dpi=300)
mpl.rcdefaults()
return
# Get indices of 5 degree field
pixsz = np.sqrt(header['CD1_1']**2 + header['CD1_2']**2)
radpix = 2.5/pixsz
ap = djs_photfrac(ypix,xpix,radpix,xdimen=xsz,ydimen=ysz)
# Smooth image
sigma = 2*radpix/2.355
if do_smooth:
smooth = gaussian_filter(image,sigma)
else:
smooth = image
# Image characteristics and plot
sig = rb.std(smooth)
med = np.median(smooth)
vmin = med - 3*sig
vmax = med + 5*sig
plt.figure(1)
plt.clf()
plt.imshow(smooth,vmin=vmin,vmax=vmax,cmap='gist_heat',interpolation='nearest', \
origin='lower')
plt.scatter(xpix,ypix,marker='+',s=100,facecolor='none',edgecolor='yellow', \
linewidth=1.5)
plt.xlim(0,xsz)
plt.ylim(0,ysz)
plt.axis('off')
plt.title('Field Center')
plt.savefig('Center.png',dpi=300)
def master_bias(files,
write=True,
outdir='/',
readnoise=False,
clobber=False,
verbose=True,
float32=True,
tag='',
median=True):
"""
Overview:
---------
Create master bias frame from series of biases (median filter).
Returns a master_bias frame and writes FITS file to disk in specified
directory.
Optionally, the read noise is calculated from the variance of each
pixel in the bias stack. This is *very* slow. So only use this option
if you really need to. The readnoise image is also written to disk.
Inputs:
-------
files : List of flat field files from which a master bias will be created.
Must be provided, no default.
Keyword arguments:
------------------
write : Toggle to write files to disk (default True)
outdir : Directory to which output files are written (default pwd)
clobber : Toggle to overwrite files if they already exist in outdir
(default False)
readnoise : Do readnoise calculation (very slow! default False)
verbose : Print out progress (default True)
Calling sequence:
-----------------
master_bias = master_bias(biasfiles,write=True,readnoise=False,
outdir='/home/users/bob/stuff/')
"""
# Don't redo master_bias unless clobber keyword set
name = outdir + 'master_bias_' + tag + '.fits'
if len(glob.glob(name)) == 1 and not clobber:
print("Master bias already exists!")
master_bias = fits.getdata(name, 0, header=False)
return master_bias
# Get information from inputs and create stack array
fct = len(files)
image, header = fits.getdata(files[0], 0, header=True)
ysz, xsz = image.shape
stack = np.zeros((fct, ysz, xsz))
temps = []
hout = header
# Load stack array and get CCD temperatures
for i in np.arange(fct):
output = '\nReading {}: frame {} of {} \r'.format(files[i].split('/')[-1], \
str(i + 1), str(fct))
sys.stdout.write(output)
sys.stdout.flush()
image, header = fits.getdata(files[i], 0, header=True)
temps.append(header["CCD-TEMP"])
stack[i, :, :] = image
# Calculate read noise directly from bias frames if prompted
if readnoise:
rn = np.zeros((ysz, xsz))
print("Starting readnoise calculation")
pbar = tqdm(desc='Calculating readnoise', total=ysz, unit='rows')
for i in np.arange(ysz):
for j in np.arange(xsz):
rn[i, j] = rb.std(stack[:, i, j])
pbar.update(1)
# Make a nice plot (after all that hard work)
aspect = np.float(xsz) / np.float(ysz)
plt.figure(39, figsize=(5 * aspect * 1.2, 5))
plt.clf()
sig = rb.std(rn)
med = np.median(rn)
mean = np.mean(rn)
vmin = med - 2 * sig
vmax = med + 2 * sig
plt.imshow(rn,
vmin=vmin,
vmax=vmax,
cmap='gist_heat',
interpolation='nearest',
origin='lower')
plt.colorbar()
plt.annotate(r'$\bar{\sigma}$ = %.2f cts' % mean, [0.95, 0.87],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large')
# path_effects=[PathEffects.SimpleLineShadow(linewidth=3,foreground="w")])
plt.annotate(r'med($\sigma$) = %.2f cts' % med, [0.95, 0.8],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.annotate(r'$\sigma_\sigma$ = %.2f cts' % sig, [0.95, 0.73],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.title("Read Noise")
plt.xlabel("pixel number")
plt.ylabel("pixel number")
if write:
plt.savefig(outdir + 'readnoise' + tag + '.png', dpi=300)
# Calculate master bias frame by median filter
print('Calculating median of stacked frames...')
if median:
master_bias = np.median(stack, axis=0)
else:
master_bias = np.mean(stack, axis=0)
# Make a plot
aspect = np.float(xsz) / np.float(ysz)
plt.figure(38, figsize=(5 * aspect * 1.2, 5))
plt.clf()
sig = rb.std(master_bias)
med = np.median(master_bias)
vmin = med - 2 * sig
vmax = med + 2 * sig
plt.imshow(master_bias,
vmin=vmin,
vmax=vmax,
cmap='gist_heat',
interpolation='nearest',
origin='lower')
plt.colorbar()
plt.annotate('Bias Level = %.2f cts' % med, [0.95, 0.87],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large',
color='k')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.annotate(r'$\sigma$ = %.2f cts' % sig, [0.95, 0.8],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.annotate(r'$\langle T_{\rm CCD} \rangle$ = %.2f C' % np.median(temps),
[0.95, 0.73],
horizontalalignment='right',
xycoords='axes fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.title("Master Bias")
plt.xlabel("pixel number")
plt.ylabel("pixel number")
# Write out bias, readnoise and plot
if write:
name = outdir + 'master_bias_' + tag
plt.savefig(name + '.png', dpi=300)
# hout = fits.Header()
hout['HISTORY'] = 'This is a median master'
hout['MCCDTEMP'] = (np.median(temps), "Median CCD temperature")
hout["TEMPSIG"] = (np.std(temps), "CCD temperature RMS")
hout["MEDBIAS"] = (med, "Median bias level (cts)")
hout["BIASSIG"] = (sig, "Bias RMS (cts)")
if len(glob.glob(name + '.fits')) == 1:
os.system('rm ' + name + '.fits')
if float32:
fits.writeto(name + '.fits', np.float32(master_bias), hout)
else:
fits.writeto(name + '.fits', master_bias, hout)
if readnoise:
name = outdir + 'readnoise' + tag
if len(glob.glob(name + '.fits')) == 1:
os.system('rm ' + name + '.fits')
if float32:
fits.writeto(name + '.fits', np.float32(rn), hout)
else:
fits.writeto(name + '.fits', rn, hout)
return master_bias
def master_dark(files,
bias=None,
write=True,
outdir='/',
clobber=False,
float32=True,
tag='',
median=True):
"""
Overview:
---------
Create master dark frame from series of darks (median filter).
Returns a master dark frame. If write is specified, a FITS file
will be written to "outdir" (default is pwd).
Inputs:
-------
files : List of flat field files from which a master dark will be created.
Must be provided, no default.
Keyword arguments:
------------------
bias : Master bias frame (default None)
write : Toggle to write files to disk (default True)
outdir : Directory to which output files are written (default pwd)
clobber : Toggle to overwrite files if they already exist in outdir
(default False)
Calling sequence:
-----------------
master_dark = master_dark(darkfiles,bias=master_bias,write=True,
outdir='/home/users/bob/stuff/')
"""
# Don't redo master_dark unless clobber keyword set
name = outdir + 'master_dark_' + tag + '.fits'
if len(glob.glob(name)) == 1 and not clobber:
print("Master dark already exists!")
master_dark = fits.getdata(name, 0, header=False)
return master_dark
# Get information from inputs and create stack array
fct = len(files)
image, header = fits.getdata(files[0], 0, header=True)
ysz, xsz = image.shape
stack = np.zeros((fct, ysz, xsz))
temps = []
exps = []
hout = header
# Load stack array and get CCD temperatures
for i in np.arange(fct):
output = '\nReading {}: frame {} of {} \r'.format(files[i].split('/')[-1], \
str(i + 1), str(fct))
sys.stdout.write(output)
sys.stdout.flush()
image, header = fits.getdata(files[i], 0, header=True)
exp = header["EXPOSURE"]
exps.append(exp)
temps.append(header["CCD-TEMP"])
# if length(bias) == 1:
# image = np.float(image)/exp
# =============================================================================
# else:
# image = (image-bias)/exp
# =============================================================================
stack[i, :, :] = image
# Obtain statistics for the master dark image header
# Temperature
tmax = np.max(temps)
tmin = np.min(temps)
tmean = np.mean(temps)
tmed = np.median(temps)
tsig = np.std(temps)
# Exposure times
expmax = np.max(exps)
expmin = np.min(exps)
print('')
print("Minimum CCD Temp. %.2f C" % tmin)
print("Maximum CCD Temp. %.2f C" % tmax)
print("CCD Temp. rms: %.3f C" % tsig)
print("CCD Temp. mean: %.2f C" % tmean)
print("CCD Temp. median: %.2f C" % tmed)
# Create master dark by median filter or mean
if median:
master_dark = np.median(stack, axis=0)
else:
master_dark = np.mean(stack, axis=0)
# Make a plot
sig = rb.std(master_dark)
med = np.median(master_dark)
vmin = med - 2 * sig
vmax = med + 2 * sig
aspect = np.float(xsz) / np.float(ysz)
plt.figure(37, figsize=(5 * aspect * 1.2, 5))
plt.clf()
plt.imshow(master_dark,
vmin=vmin,
vmax=vmax,
cmap='gist_heat',
interpolation='nearest',
origin='lower')
plt.colorbar()
plt.annotate('Dark Current = %.2f cts' % med, [0.72, 0.8],
horizontalalignment='right',
xycoords='figure fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.annotate(r'$\sigma$ = %.2f cts' % sig, [0.72, 0.75],
horizontalalignment='right',
xycoords='figure fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.annotate(r'$\langle T_{\rm CCD} \rangle$ = %.2f C' % np.median(temps),
[0.72, 0.7],
horizontalalignment='right',
xycoords='figure fraction',
fontsize='large')
# path_effects=[PathEffects.withStroke(linewidth=3,foreground="w")])
plt.title("Master Dark")
plt.xlabel("pixel number")
plt.ylabel("pixel number")
# Write out plot and master dark array
if write:
name = outdir + 'master_dark_' + tag
plt.savefig(name + '.png', dpi=300)
# hout = fits.Header()
hout['HISTORY'] = 'This is a median master'
hout["TEMPMAX"] = (tmax, "Maximum CCD temperature")
hout["TEMPMIN"] = (tmin, "Minimum CCD temperature")
hout["TEMPMED"] = (tmed, "Median CCD temperature")
hout["TEMPMN"] = (tmean, "Mean CCD temperature")
hout["TEMPSIG"] = (tsig, "CCD temperature RMS")
hout["EXPMAX"] = (expmax, "Maximum exposure time")
hout["EXPMIN"] = (expmin, "Minimum exposure time")
hout["DARKCNT"] = (med, "Median dark current (cts)")
hout["DARKSIG"] = (sig, "Dark current RMS (cts)")
if len(glob.glob(name)) == 1:
os.system('rm ' + name + '.fits')
if float32:
fits.writeto(name + '.fits', np.float32(master_dark), hout)
else:
fits.writeto(name + '.fits', master_dark, hout)
return master_dark
def master_flat(files,
bias=None,
dark=None,
write=True,
outdir='/',
tag='',
clobber=False,
stretch=3,
float32=True,
median=True):
"""
Overview:
---------
Create a master flat using (optionally) a provided bias and dark frame. Output
is written to "outdir" in FITS format.
Inputs:
-------
files : List of flat field files from which a master flat will be created.
Must be provided, no default.
Keyword arguments:
------------------
bias : Master bias frame (default None)
dark : Master dark frame calibrated in ADU/sec (default None)
band : Band from which flatis being produced
write : Toggle to write files to disk (default True)
outdir : Directory to which output files are written (default pwd)
clobber : Toggle to overwrite files if they already exist in outdir
(default False)
stretch : Multiple of the noise RMS to stretch image (default 3)
Calling sequence:
-----------------
master_flat = master_flat(flatfiles,bias=master_bias,dark=master_dark,write=True,
outdir='/home/users/bob/stuff/')
"""
# Don't redo master_flat unless clobber keyword set
name = outdir + 'master_flat_' + tag + '.fits'
if len(glob.glob(name)) == 1 and not clobber:
print("Master flat already exists!")
master_flat = fits.getdata(name, 0, header=False)
return master_flat
# Get information from inputs and create stack array
fct = len(files)
image, header = fits.getdata(files[0], 0, header=True)
filter = header["filter"]
ysz, xsz = image.shape
stack = np.zeros((fct, ysz, xsz))
hout = header
# Load stack array and get CCD temperatures
meds = []
for i in np.arange(fct):
output = '\nReading {}: frame {} of {} \r'.format(files[i].split('/')[-1], \
str(i + 1), str(fct))
sys.stdout.write(output)
sys.stdout.flush()
image, header = fits.getdata(files[i], 0, header=True)
image = np.float32(image)
if header["filter"] != filter:
sys.exit("Filters do not match!")
# =============================================================================
# if length(bias) > 1:
# image -= bias
# if length(dark) > 1:
# exptime = header['EXPTIME']
# image -= dark*exptime
# =============================================================================
meds.append(np.median(image))
# stack[i, :, :] = image / np.median(image)
stack[i, :, :] = image
# Obtain statistics for the master dark image header
med = np.median(meds)
sig = np.std(meds)
# Create master flat by median filter
if median:
master_flat = np.median(stack, axis=0)
else:
master_flat = np.mean(stack, axis=0)
# Make a plot
sig = rb.std(master_flat)
med = np.median(master_flat)
vmin = med - stretch * sig
vmax = med + stretch * sig
aspect = np.float(xsz) / np.float(ysz)
plt.figure(40, figsize=(5 * aspect * 1.2, 5))
plt.clf()
plt.imshow(master_flat,
vmin=vmin,
vmax=vmax,
cmap='gist_heat',
interpolation='nearest',
origin='lower')
plt.colorbar()
plt.title("Master Flat")
plt.xlabel("pixel number")
plt.ylabel("pixel number")
# Write out plot and master flat array
if write:
plt.savefig(outdir + 'master_flat' + tag + '.png', dpi=300)
# hout = fits.Header()
hout['HISTORY'] = 'This is a median master'
hout["FILTER"] = (filter, "Filter used when taking image")
hout["MEDCTS"] = (med, "Median counts in individual flat frames")
hout["MEDSIG"] = (sig, "Median count RMS in individual flat frames")
# =============================================================================
# if length(bias) > 1:
# hout.add_comment("Bias subtracted")
# if length(dark) > 1:
# hout.add_comment("Dark subtracted")
# =============================================================================
if len(glob.glob(outdir + 'master_flat' + tag + '.fits')) == 1:
os.system('rm ' + outdir + 'master_flat' + tag + '.fits')
if float32:
fits.writeto(outdir + 'master_flat_' + tag + '.fits',
np.float32(master_flat), hout)
else:
fits.writeto(outdir + 'master_flat_' + tag + '.fits', master_flat,
hout)
return master_flat