def run(path0, silent=False, verbose=True):
'''
Main function to run for a given path containing the raw GNIRS data
Parameters
----------
path0 : str
Path to raw FITS file. Must include '/' at the end
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 22 March 2017
Modified by Chun Ly, 23 March 2017
- Call dir_check.main() to handle multiple date directories
Modified by Chun Ly, 8 January 2018
- Import glog and call for stdout and ASCII logging
- Pass mylogger to get_files()
Modified by Chun Ly, 7 May 2018
- Bug fix: Call check_path() to add '/' in path0
'''
rawdir = check_path(path0) # + on 07/05/2018
# + on 08/01/2018
logfile = path0+'symlink.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin run : '+systime())
# + on 23/03/2017
dir_list, list_path = dir_check.main(path0, mylogger=mylogger,
silent=silent, verbose=verbose)
# Mod on 23/03/2017
for path in list_path:
files, n_files = get_files(path, mylogger=mylogger, silent=silent,
verbose=verbose)
for nn in xrange(n_files):
c_file = path+'c'+files[nn]
if exists(c_file):
mylogger.warn('File exists : '+c_file)
else:
cmd0 = 'ln -fs '+files[nn]+' '+c_file
if silent == False:
mylogger.info(cmd0)
os.system(cmd0)
#endfor
#endfor
if silent == False: mylogger.info('### End run : '+systime())
def main(path0, silent=True, verbose=False):
'''
Main function for checking paths and adding '/'
Parameters
----------
path0 : str
Full path.
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 20 September 2017
'''
if silent == False: log.info('### Begin main : '+systime())
if path0[-1] != '/': path0 = path0 + '/'
if silent == False: log.info('### End main : '+systime())
return path0
def in_bino_field(tab0, verts0, silent=False, verbose=True):
'''
Determine sources in MMT/Binospec field
Parameters
----------
tab0 : astropy.table.table.Table
Astropy Table of HSC-SSP NB excess emitter catalog.
verts0 : list
List of matplotlib.patches.Rectangle vertices
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
in_fields0 : list
List of numpy arrays
Notes
-----
Created by Chun Ly, 22 March 2018
'''
if silent == False: log.info('### Begin in_bino_field : ' + systime())
ra = tab0['ra'].data
dec = tab0['dec'].data
coords = np.array([ra, dec]).transpose()
n_ptgs = len(verts0)
in_field0 = []
for cc in range(n_ptgs):
# Side 1
t_path1 = Path0(verts0[cc][0])
cp_res1 = t_path1.contains_points(coords)
in_field1 = np.array(
[xx for xx in range(len(tab0)) if cp_res1[xx] == True])
# Side 2
t_path2 = Path0(verts0[cc][1])
cp_res2 = t_path2.contains_points(coords)
in_field2 = np.array(
[xx for xx in range(len(tab0)) if cp_res2[xx] == True])
print cc, len(in_field1), len(in_field2)
in_field = np.append(in_field1, in_field2)
in_field.sort()
in_field0.append(in_field)
#endfor
if silent == False: log.info('### End in_bino_field : ' + systime())
return in_field0
def main(path, final_prefix, outfile='', all_lis=[], all_file='',
mylogger=None, silent=False, verbose=True):
'''
Check if files exist. If not, create a temporary ASCII file to execute
IRAF commands for the subset of files that do not exists
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 26 April 2017
Modified by Chun Ly, 10 January 2018
- Implement glog logging, allow mylogger keyword input
'''
# + on 10/01/2018
if type(mylogger) == type(None):
mylog, clog = 0, log
else:
mylog, clog = 1, mylogger
if silent == False: clog.info('### Begin main : '+systime())
if len(all_lis) == 0 and all_file == '':
clog.warn('Must specify all_lis or all_file')
clog.warn('Aborting!!!')
return
#endif
if len(all_lis) == 0:
all_lis = np.loadtxt(path+'all.lis', dtype=type(str))
no_files = [file0 for file0 in all_lis if
exists(path+final_prefix+file0) == False]
if len(no_files) > 0:
if outfile != '':
if silent == False: clog.info('Writing : '+path+outfile)
np.savetxt(path+outfile, no_files, fmt='%s')
else:
pref_name = [final_prefix+file0 for file0 in no_files]
print pref_name
if silent == False: clog.info('### End main : '+systime())
def get_files(path0, mylogger=None, silent=False, verbose=True):
'''
Simple function to get names of raw files
Parameters
----------
path0 : str
Path to raw FITS file. Must include '/' at the end
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
files : list
List containing the filename for FITS raw files
n_files : int
Size of [files]
Notes
-----
Created by Chun Ly, 22 March 2017
Modified by Chun Ly, 5 June 2017
- Fix minor bug: infile -> infile0
Modified by Chun Ly, 8 January 2018
- Import glog and call for stdout and ASCII logging
Modified by Chun Ly, 20 April 2018
- Bug fix: mylog -> clog
'''
if type(mylogger) == type(None):
mylog, clog = 0, log
else:
mylog, clog = 1, mylogger
if silent == False: clog.info('### Begin get_files : '+systime())
infile0 = path0+'all.lis'
if not exists(infile0):
clog.warn('File does not exists!!! : '+infile0)
clog.warn('EXITING!!!')
return
if silent == False:
clog.info('Reading : '+infile0)
files = np.loadtxt(infile0, dtype=type(str)).tolist()
n_files = len(files)
if silent == False: clog.info('### End get_files : '+systime())
return files, n_files
def main(sub_dict0, fld_idx, fld_tab, Inst, tab_outfile, silent=False,
verbose=True):
'''
Provide explanation for function here.
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 21 March 2018
- Bug fix: with removing PA column in table
'''
if silent == False: log.info('### Begin main : '+systime())
for key in sub_dict0.keys():
s_idx = sub_dict0[key]
cmd1 = 'n_fld_%s = np.zeros(len(fld_idx), dtype=np.int)' % key
exec(cmd1)
for ff,in_field in enumerate(fld_idx):
in_idx = list(set(in_field.tolist()) & set(s_idx))
cmd2 = 'n_fld_%s[ff] = len(in_idx)' % key
exec(cmd2)
#endfor
#endfor
t_cols = ['n_fld_'+ aa for aa in sub_dict0.keys()]
fld_arr0 = [fld_tab['MaskName'].data, fld_tab['RA'].data,
fld_tab['Dec'].data, fld_tab['PA'].data]
names0 = ['MaskName', 'RA', 'Dec', 'PA']
cmd3 = "fld_arr0 += ["+', '.join(t_cols)+']'
exec(cmd3)
names0 += [val.replace('NB0','NB') for val in sub_dict0.keys()]
inptg_tab0 = Table(fld_arr0, names=names0)
if Inst == 'Hecto': del inptg_tab0['PA']
if silent == False: inptg_tab0.pprint(max_lines=-1)
if silent == False: log.info('### Writing : '+tab_outfile)
inptg_tab0.write(tab_outfile, format='ascii.latex')
if silent == False: log.info('### End main : '+systime())
def in_deimos_field(tab0, verts0, silent=False, verbose=True):
'''
Determine sources in Keck/DEIMOS field
Parameters
----------
tab0 : astropy.table.table.Table
Astropy Table of HSC-SSP NB excess emitter catalog.
verts0 : list
List of matplotlib.patches.Rectangle vertices
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
in_fields0 : list
List of numpy arrays
Notes
-----
Created by Chun Ly, 3 March 2018
Modified by Chun Ly, 4 March 2018
- Bug fix: Incorrect variable name, patches -> verts0
'''
if silent == False: log.info('### Begin in_deimos_field : ' + systime())
ra = tab0['ra'].data
dec = tab0['dec'].data
coords = np.array([ra, dec]).transpose()
n_ptgs = len(verts0)
in_field0 = []
for cc in range(n_ptgs):
t_path = Path0(verts0[cc])
cp_res = t_path.contains_points(coords)
in_field = np.array(
[xx for xx in range(len(tab0)) if cp_res[xx] == True])
print cc, len(in_field)
in_field0.append(in_field)
#endfor
if silent == False: log.info('### End in_deimos_field : ' + systime())
return in_field0
def cp_files(outdir,
path,
final_prefix,
input_lis,
silent=False,
verbose=True):
'''
Copy files into outdir for certain IRAF functions
Parameters
----------
outdir : str
Full path for where files are temporarily stored.
Must include '/' at the end
path : str
Full path to list. Must include '/' at the end
final_prefix : str
Files with specific prefix to search for ('rnc', etc).
This will be added before the filenames in [input_lis]
input_lis : str
Filename for input list to check ('arc.lis', 'flat.lis', etc.)
Full path need to be provided here.
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 7 May 2017
'''
if silent == False: log.info('### Begin cp_files : ' + systime())
if silent == False: log.info('### Reading : ' + input_lis)
files = np.loadtxt(input_lis, dtype=type(str))
files0 = [path + final_prefix + file0 for file0 in files]
cmd0 = 'cp -a ' + ' '.join(files0) + ' ' + outdir
if silent == False: log.info('### ' + cmd0)
os.system(cmd0)
if silent == False: log.info('### End cp_files : ' + systime())
def run_all(files=None, path0=None, user='******', passwd='',
silent=False, verbose=True):
'''
Run all functions related to MMTCam analysis
Parameters
----------
files : list
List of files
path0 : string
Path to files. If not provided it is assumed that [files] has the full
path name
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 23 February 2017
Modified by Chun Ly, 28 February 2017
- Add user and passwd keyword to pass on to make_postage()
'''
if files == None and path0 == None:
log.error('files and path0 keywords not provided')
log.error('Exiting!!!')
return
if silent == False: log.info('### Begin run_all: '+systime())
if files == None and path0 != None:
files, seqno = get_files(path0)
# path0 = None # Reset since files will have full path
if silent == False:
log.info('The following files will be analyzed from : ')
log.info(path0)
for file in files: log.info(os.path.basename(file))
find_stars(files=files, path0=path0, plot=True, verbose=False)
make_postage(files=files, path0=path0, user=user, passwd=passwd,
verbose=False)
psf_contours(files=files, path0=path0, verbose=False)
if silent == False: log.info('### End run_all: '+systime())
def in_hecto_field(tab0, fld_coord, silent=False, verbose=True):
'''
Determine sources in MMT/Hectospec field
Parameters
----------
tab0 : astropy.table.table.Table
Astropy Table of HSC-SSP NB excess emitter catalog.
fld_coord : list
List of RA,Dec coordinate set
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
in_fields0 : list
List of numpy arrays
Notes
-----
Created by Chun Ly, 16 March 2018
'''
if silent == False: log.info('### Begin in_hecto_field : '+systime())
ra = tab0['ra'].data
dec = tab0['dec'].data
n_ptgs = len(fld_coord)
in_field0 = []
for cc in range(n_ptgs):
ra_diff0 = ra - fld_coord[cc][0]
dec_diff0 = dec - fld_coord[cc][1]
diff0 = np.sqrt(ra_diff0**2 + dec_diff0**2)
in_field = np.array([xx for xx in range(len(tab0)) if
diff0[xx] <= 0.50])
print cc, len(in_field)
in_field0.append(in_field)
#endfor
if silent == False: log.info('### End in_hecto_field : '+systime())
return in_field0
def delete(path0, silent=False, verbose=True):
'''
Remove all symbolic links in given path containing the raw GNIRS data
Parameters
----------
path0 : str
Path to raw FITS file. Must include '/' at the end
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 22 March 2017
Modified by Chun Ly, 8 January 2018
- Import glog and call for stdout and ASCII logging
- Pass mylogger to get_files()
Modified by Chun Ly, 22 January 2018
- Pass rm command strings to mylogger
'''
# + on 08/01/2018
logfile = path0+'symlink.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin delete : '+systime())
files, n_files = get_files(path0, mylogger=mylogger, silent=silent,
verbose=verbose)
for nn in xrange(n_files):
c_file = path0+'c'+files[nn]
if exists(c_file):
if os.path.islink(c_file) == True:
cmd0 = 'rm '+c_file
mylogger.info(cmd0)
os.system(cmd0)
else:
mylogger.info('File is from cleanir: '+c_file)
if silent == False: mylogger.info('### End delete : '+systime())
def main(field='', dr='pdr1', silent=False, verbose=True):
'''
Main function to read in HSC SSP catalogs of NB excess emitters
Parameters
----------
field : str
Name of field to read in. Either 'udeep' or 'deep'
dr : str
Data release name. Default: 'pdr1'
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 27 February 2018
Modified by Chun Ly, 2 March 2018
- Call paths module to get path
'''
if silent == False: log.info('### Begin main : ' + systime())
if field == '':
log.warn("### [field] input not specified!!!")
log.warn("### Either 'udeep' or 'deep'")
log.warn('### Exiting!!!')
return
dir0 = paths.gdrive() # Mod on 02/03/2018
infile = dir0 + 'catalogs/%s_%s_nb_forced_coord_phot.csv.gz' % (dr, field)
if silent == False: log.info('### Reading : ' + infile)
tab0 = asc.read(infile, format='csv')
if silent == False: log.info('### End main : ' + systime())
return tab0
def main(silent=False, verbose=True):
'''
Provide explanation for function here.
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 13 July 2018
'''
if silent == False: log.info('### Begin main : ' + systime())
path0 = '/Users/cly/Google Drive/NASA_Summer2015/Filters/'
filters = ['NB704', 'NB711', 'NB816', 'NB921', 'NB973']
files = [path0 + filt + 'response.dat' for filt in filters]
filt_corr = np.zeros(len(files))
for ff in range(len(files)):
log.info('Reading : ' + files[ff])
tab1 = asc.read(files[ff], format='no_header')
y_val = tab1['col2']
y_val /= max(y_val)
good = np.where(y_val >= 0.05)[0]
# Compute statistical correction by Sum [filter_amp * filter_amp] / Sum [filter_amp]
weight_sum = np.sum(y_val[good]**2) / np.sum(y_val[good])
filt_corr[ff] = 1 / weight_sum
filt_tab = Table([filters, filt_corr], names=('Filter', 'Filt_Stat_Corr'))
filt_tab.pprint()
if silent == False: log.info('### End main : ' + systime())
def get_k_values(wave, law='CCM89', silent=True, verbose=False):
'''
Function to get k(lambda):
A(lambda) = k(lambda) * E(B-V)
Parameters
----------
wave : float or array like
Wavelength in units of Angstroms
law : string
String for dust attenuation "law". Default: "CCM89".
Full list available from RC.getLaws()
Options are:
'G03 LMC', 'K76', 'F99-like', 'F88 F99 LMC', 'No correction',
'SM79 Gal', 'MCC99 FM90 LMC', 'CCM89 Bal07', 'CCM89 oD94',
'S79 H83 CCM89', 'F99', 'CCM89'
- See pn.RedCorr.printLaws() for more details
silent : boolean
Turns off stdout messages. Default: True
verbose : boolean
Turns on additional stdout messages. Default: False
Returns
-------
k value at wave
Notes
-----
Created by Chun Ly, 22 November 2016
'''
if silent == False:
print '### Begin balmer_decrement.get_k_values() | '+systime()
RC = pn.RedCorr(E_BV = 1.0)
RC.law = law
if silent == False:
print '### End balmer_decrement.get_k_values() | '+systime()
return np.log10(RC.getCorr(wave)) / 0.4
def rm_files(final_prefix, input_lis, silent=False, verbose=True):
'''
Delete files in the current directory
Parameters
----------
final_prefix : str
Files with specific prefix to search for ('rnc', etc).
This will be added before the filenames in [input_lis]
input_lis : str
Filename for input list to check ('arc.lis', 'flat.lis', etc.)
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 7 May 2017
Modified by Chun Ly, 15 May 2017
- Got rid of [path] array
'''
if silent == False: log.info('### Begin rm_files : ' + systime())
if silent == False: log.info('### Reading : ' + input_lis)
files = np.loadtxt(input_lis, dtype=type(str))
files0 = [final_prefix + file0 for file0 in files]
cmd0 = 'rm ' + ' '.join(files0)
if silent == False: log.info('### ' + cmd0)
os.system(cmd0)
if silent == False: log.info('### End rm_files : ' + systime())
def main(path0, out_pdf='', silent=False, verbose=True, overwrite=False):
'''
Main function to generate PDF illustrating alignment on target
Parameters
----------
path0 : str
Path to FITS file. Must include '/' at the end
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
overwrite : boolean
Overwrite files if they exists. Default: False
Returns
-------
Notes
-----
Created by Chun Ly, 24 March 2017
Modified by Chun Ly, 01 April 2017
- Handle CRs and bad pixels using cosmicrays_lacosmic
Modified by Chun Ly, 04 April 2017
- Use find_gnirs_window_mean to find center
Modified by Chun Ly, 04-05 April 2017
- Adjust greyscale limits to handle slit image (make it black),
and faint sources
Use find_gnirs_window_mean to find center
Modified by Chun Ly, 05 April 2017
- Handle alignment sequences with more than just 4 frames
- Handle excess subplots for individual PDF pages (remove axes)
- Compute seeing FWHM for acquisition images
Modified by Chun Ly, 06 April 2017
- Get coordinates for slit in cutout
Modified by Chun Ly, 11 May 2017
- Use slit image to find center when telluric data is only available
Modified by Chun Ly, 3 July 2017
- Add overwrite option to prevent overwriting file
Modified by Chun Ly, 9 January 2018
- Import glog and call for stdout and ASCII logging
- Pass mylogger to find_gnirs_window_mean(), find_gnirs_window()
Modified by Chun Ly, 20 April 2018
- Pass mylogger to gauss2d_fit()
- Switch print statements to mylogger calls
Modified by Chun Ly, 22 April 2018
- Bug fix: mylogger calls mistakes
- Bug fix: mylogger calls mistakes (cont'd)
'''
# + on 09/01/2018
logfile = path0 + 'align_check.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin main : ' + systime())
dir_list, list_path = dir_check.main(path0,
mylogger=mylogger,
silent=silent,
verbose=verbose)
out_pdf_default = out_pdf
for path in list_path:
infile = path + 'hdr_info.QA.tbl'
if not exists(infile):
mylogger.warning('File does not exist : ' + infile)
mylogger.warning('Exiting!!! ' + systime())
return
out_pdf = path + 'align_check.pdf' if out_pdf == '' else path + out_pdf
# Mod on 03/07/2017
if overwrite == False and exists(out_pdf):
mylogger.warn('File exists!! Will not overwrite ' + out_pdf)
else:
pp = PdfPages(out_pdf)
if silent == False: mylogger.info('Reading: ' + infile)
tab0 = asc.read(infile, format='fixed_width_two_line')
align = [ii for ii in xrange(len(tab0)) if tab0['QA'][ii] == 'N/A']
if silent == False:
mylogger.info('Number of alignment images found : ' +
str(len(align)))
ID = tab0['object'][align]
ID0 = list(set(ID)) #Unique ID's
if silent == False:
mylogger.info('Sources found : ' + ', '.join(ID0))
# + on 04/04/2017
win_ref_idx = [
tt for tt in xrange(len(tab0))
if (tab0['QA'][tt] == 'N/A') and ('Acq' in tab0['slit'][tt])
and ('HIP' not in tab0['object'][tt]) and (
'HD' not in tab0['object'][tt])
]
# Mod on 11/05/2017
if len(win_ref_idx) > 0:
win_ref_file = path + tab0['filename'][win_ref_idx[0]]
mylogger.info('Reference image for finding GNIRS window : ' +
win_ref_file)
x_min, x_max, y_min, y_max, x_cen, \
y_cen = find_gnirs_window_mean(win_ref_file, mylogger=mylogger)
else:
mylogger.info('Using telluric image as reference')
win_ref_file = path + tab0['filename'][0]
slit_x0, slit_y0_lo, slit_y0_hi = get_slit_trace(win_ref_file)
x_min, x_max = min(slit_x0), max(slit_x0)
x_cen = (x_min + x_max) / 2.0
y_cen = (np.median(slit_y0_lo) + np.median(slit_y0_hi)) / 2.0
y_min, y_max = y_cen - size2d[0].value / 2.0, y_cen + size2d[
0].value / 2.0
pos_cen = (x_cen, y_cen)
new_size = u.Quantity((y_max - y_min, x_max - x_min), u.pixel)
# + on 20/04/2018, Mod on 22/04/2018
mylogger.info('pos_cen : (%f, %f) ' % (pos_cen[0], pos_cen[1]))
mylogger.info('new_size : [%f, %f] pix ' %
(new_size[0].value, new_size[1].value))
for ii in xrange(len(ID0)):
t_idx = [
tt for tt in xrange(len(tab0)) if
(tab0['object'][tt] == ID0[ii] and tab0['QA'][tt] == 'N/A')
]
t_files = [path + a for a in tab0['filename'][t_idx]]
ncols = 2.0
nrows = 2 # np.ceil(len(t_idx)/ncols)
ncols, nrows = np.int(ncols), np.int(nrows)
# Mod on 05/04/2017
if len(t_idx) <= nrows * ncols:
fig, ax_arr = plt.subplots(nrows=nrows, ncols=ncols)
#med0, x_min, x_max, y_min, \
# y_max, x_cen, y_cen = find_gnirs_window(t_files[1], mylogger=mylogger)
# Later + on 24/03/2017 | Mod on 04/04/2017
xcen, ycen = find_star(t_files[-1],
pos=pos_cen,
find_size2d=new_size)
# Fix to get relative coordinate for Cutout2D image
#xcen -= pos_cen[0]-new_size[1].value/2.0
#ycen -= pos_cen[1]-new_size[0].value/2.0
slit_x0, slit_y0_lo, slit_y0_hi = get_slit_trace(
t_files[0]) #, x_min, x_max)
# Adjust values for offset that is applied
# Bug: Mod on 04/04/2017 to get proper coordinate
slit_x0 -= np.int64(pos_cen[0] - size2d[1].value / 2.0)
slit_y0_lo -= pos_cen[1] - size2d[0].value / 2.0
slit_y0_hi -= pos_cen[1] - size2d[0].value / 2.0
for jj in xrange(len(t_idx)):
jj_idx = t_idx[jj]
# + on 05/04/2017
if len(t_idx) > (nrows * ncols):
if jj % (nrows * ncols) == 0:
fig, ax_arr = plt.subplots(nrows=nrows,
ncols=ncols)
im0 = fits.getdata(t_files[jj])
hdr0 = fits.getheader(t_files[jj], ext=0) # Get WCS header
# + 01/04/2017
im0_clean = cosmicray_lacosmic(im0, sigclip=10)[0]
cutout = Cutout2D(im0_clean,
pos_cen,
size2d,
mode='partial',
fill_value=np.nan)
t_col, t_row = jj % ncols, (jj / ncols) % nrows
# Mod on 04/04/2017 to handle bright and faint stars
max0 = np.max(cutout.data)
# Compute median within GNIRS window
# + on 04-05/04/2017
temp = im0_clean[-50:-1, :]
bgd0, sig0 = np.median(temp), np.std(temp)
idx_y, idx_x = np.where(im0_clean > (bgd0 + 5 * sig0))
med0 = np.median(im0_clean[idx_y, idx_x])
mylogger.info('## max0 : %f med0 : %f ' % (max0, med0))
if max0 > 50000:
z1, z2 = zscale.get_limits(cutout.data)
z2 = max0 # Change for better stretch for telluric star
else:
if ('Acq_' not in tab0['slit'][jj_idx]) and \
(tab0['exptime'][jj_idx] == 3):
# First frame that will show the longslit
z1, z2 = 0.0, 0.5 * max0
else:
# This should handle faint and bright stars
z1, z2 = 0.5 * med0, max0
norm = ImageNormalize(vmin=z1, vmax=z2)
t_ax = ax_arr[t_row, t_col]
t_ax.imshow(cutout.data,
cmap='Greys',
origin='lower',
norm=norm)
#aplpy.FITSFigure(cutout)
# Draw trace of slit
t_ax.plot(slit_x0, slit_y0_lo, 'r-')
t_ax.plot(slit_x0, slit_y0_hi, 'r-')
t_ax.xaxis.set_ticklabels([])
t_ax.yaxis.set_ticklabels([])
fig.suptitle(path, fontsize=14)
txt0 = tab0['filename'][jj_idx] + '\n'
txt0 += tab0['datelabel'][jj_idx] + '\n'
txt0 += tab0['UT_date'][jj_idx] + '\n'
txt0 += tab0['object'][jj_idx]
t_ax.annotate(txt0, [0.025, 0.95],
xycoords='axes fraction',
ha='left',
va='top')
# Plot inset | Later + on 24/03/2017
axins = zoomed_inset_axes(t_ax, 6, loc=4)
norm2 = ImageNormalize(vmin=z1, vmax=z2)
axins.imshow(cutout.data,
cmap='Greys',
origin='lower',
norm=norm2)
# Draw trace of slit
axins.plot(slit_x0, slit_y0_lo, 'r-')
axins.plot(slit_x0, slit_y0_hi, 'r-')
# Mod on 04/04/2017 to get Cutout2d coordinates
c_xcen = xcen - (pos_cen[0] - size2d[1].value / 2.0)
c_ycen = ycen - (pos_cen[1] - size2d[0].value / 2.0)
x1, x2, y1, y2 = c_xcen - 20, c_xcen + 20, c_ycen - 20, c_ycen + 20
axins.set_xlim([x1, x2])
axins.set_ylim([y1, y2])
axins.xaxis.set_ticklabels([])
axins.yaxis.set_ticklabels([])
mark_inset(t_ax,
axins,
loc1=1,
loc2=3,
fc="none",
ec="b",
ls='dotted',
lw=0.5)
# Compute FWHM of alignment star | + on 05/04/2017
if ('Acq_' not in tab0['slit'][jj_idx]) and \
(tab0['exptime'][jj_idx] == 3):
mylogger.info('No source in slit : ' +
tab0['filename'][jj_idx])
else:
# + on 06/04/2017
c_size2d = u.Quantity((40, 40), u.pixel)
c_slit_x0 = slit_x0 - (c_xcen -
c_size2d[1].value / 2.0)
c_slit_y0_lo = slit_y0_lo - (c_ycen -
c_size2d[0].value / 2.0)
c_slit_y0_hi = slit_y0_hi - (c_ycen -
c_size2d[0].value / 2.0)
im0_crop = Cutout2D(cutout.data, (c_xcen, c_ycen),
c_size2d,
mode='partial',
fill_value=np.nan)
gauss2d_fit(im0_crop.data,
hdr0,
t_ax,
c_slit_x0,
c_slit_y0_lo,
c_slit_y0_hi,
mylogger=mylogger) # Mod on 06/04/2017
# Write each page separately | + on 05/04/2017
if len(t_idx) > (nrows * ncols):
# Mod later on 05/04/2017 to handle excess subplots
if jj == len(t_idx) - 1:
rem0 = len(t_idx) % (nrows * ncols) # remainder
if rem0 != 0:
for rr in range(rem0, nrows * ncols, 1):
t_col, t_row = rr % ncols, (rr /
ncols) % nrows
ax_arr[t_row, t_col].axis('off')
if (jj % (nrows * ncols) == nrows*ncols-1) or \
(jj == len(t_idx)-1):
subplots_adjust(left=0.02,
bottom=0.02,
top=0.95,
right=0.98,
wspace=0.02,
hspace=0.02)
fig.set_size_inches(11, 8)
fig.savefig(pp, format='pdf')
#endfor
# Mod on 05/04/2017
if len(t_idx) <= nrows * ncols:
# Mod later on 05/04/2017 to handle excess subplots
for rr in range(len(t_idx), nrows * ncols):
t_col, t_row = rr % ncols, (rr / ncols) % nrows
ax_arr[t_row, t_col].axis('off')
subplots_adjust(left=0.02,
bottom=0.02,
top=0.95,
right=0.98,
wspace=0.02,
hspace=0.02)
fig.set_size_inches(11, 8)
fig.savefig(pp, format='pdf')
#endfor
pp.close()
#endelse
out_pdf = out_pdf_default
if silent == False: mylogger.info('### End main : ' + systime())
def main(path0='',
out_pdf='',
check_quality=True,
skysub=False,
silent=False,
verbose=True,
overwrite=False):
'''
main() function to compute natural seeing (image quality) from bright
alignment star
Parameters
----------
path0 : str
Full path to where output PDF and FITS file are located. Must end
with a '/'
out_pdf : str
Filename for output PDF. Do NOT include full path
check_quality : boolean
Check whether data meets IQ requirements. Default: True
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
overwrite : boolean
Overwrite files if they exists. Default: False
Returns
-------
multi-page PDF plot
Notes
-----
Created by Chun Ly, 10 March 2017
- Later modified to include check_quality keyword option
- Later modified to include inset that shows the stacked line profile
Modified by Chun Ly, 11 April 2017
- Call dir_check.main() to handle multiple date directories
Modified by Chun Ly, 13 April 2017
- Minor bug: Check if file exists first
Modified by Chun Ly, 10 May 2017
- Minor bug: When .lis file contains only one entry, problem for
appending to list
Modified by Chun Ly, 1 June 2017
- Added overwrite keyword option to overwrite file. Default is not to
overwrite .pdf files
- Bug found: No longer need sky.lis since obj.lis includes all
Modified by Chun Ly, 6 June 2017
- Add skysub keyword option to operate on sky-subtracted images
Modified by Chun Ly, 14 July 2017
- Fix tick mark locations
- Fix y limit range for extreme outliers
Modified by Chun Ly, 16 November 2017
- Change prefix: rnc to rbnc
Modified by Chun Ly, 18 December 2017
- Import glog and call for stdout and ASCII logging
- Pass mylogger to compute_fwhm()
Modified by Chun Ly, 11 January 2018
- Pass mylogger to dir_check.main()
Modified by Chun Ly, 18 April 2018
- Compute and report seeing at zenith
- Show FWHM @ Zenith on right y-axis
Modified by Chun Ly, 19 April 2018
- Include airmass info in plots
Modified by Chun Ly, 14 May 2018
- Write ASCII table containing FWHM determination
Modified by Chun Ly, 18 May 2018
- Adjust subplots_adjust to avoid labels being cut off
- Handle case when extra plot window (odd numbers) is available
- Handle case with extra plot window (cont'd)
Modified by Chun Ly, 19 May 2018
- Include QA (PASS/USABLE/FAIL) info in table
Modified by Chun Ly, 28 June 2018
- Bug troubleshooting with ValueError
- Handle ValueError for avg FWHM
'''
# + on 18/12/2017
logfile = path0 + 'IQ_plot.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin main : ' + systime())
# + on 11/04/2017
dir_list, list_path = dir_check.main(path0,
mylogger=mylogger,
silent=silent,
verbose=verbose)
out_pdf_default = out_pdf
# Mod on 11/04/2017
for path in list_path:
files = []
file_lis = ['obj.lis', 'telluric.lis'] # Minor bug fix on 01/06/2017
for file0 in file_lis:
# Mod on 13/04/2017
if exists(path + file0):
if silent == False: mylogger.info('Reading : ' + path + file0)
t_files = np.loadtxt(path + file0, dtype=type(str)).tolist()
# Bug fix - 10/05/2017
if type(t_files) == str: t_files = [t_files]
files += t_files
else:
if silent == False:
mylogger.info('File not found : ' + path + file0)
files.sort()
n_files = len(files)
# + on 14/05/2018
FWHM_avg_arr = np.zeros(n_files) # FWHM from averaging stack0_shift
FWHM_avg_arr_Z = np.zeros(
n_files) # FWHM from averaging stack0_shift at Zenith
FWHM_avg_QA = [
''
] * n_files # QA check from averaging stack0_shift at Zenith
FWHM_med_arr = np.zeros(n_files) # FWHM from median along Y
FWHM_med_arr_Z = np.zeros(
n_files) # FWHM from median along Y at Zenith
FWHM_med_QA = [''] * n_files # QA check from median along Y at Zenith
# Mod on 06/06/2017
if skysub == True:
files = ['brnc' + file0 for file0 in files] # Mod on 16/11/2017
out_pdf = path+'IQ_plot.skysub.pdf' if out_pdf == '' else \
path+out_pdf
else:
out_pdf = path+'IQ_plot.raw.pdf' if out_pdf == '' else \
path+out_pdf
if overwrite == False and exists(out_pdf):
mylogger.warn('File exists!! Will not overwrite ' + out_pdf)
else:
pp = PdfPages(out_pdf)
for nn in xrange(n_files):
if silent == False: mylogger.info('Reading : ' + files[nn])
hdr0 = fits.getheader(path + files[nn])
# Mod on 06/06/2017
if skysub == False:
im0 = fits.getdata(path + files[nn])
else:
im0 = fits.getdata(path + files[nn], 'sci')
airmass = hdr0['AIRMASS'] # + on 18/04/2018
# Mod on 18/12/2017
bins, fwhm0, stack0_shift = compute_fwhm(im0,
mylogger=mylogger)
row = nn % 2
if row == 0: fig, ax0 = plt.subplots(2, 1)
good = np.where(fwhm0 > 0)[0]
ax0[row].plot(bins[good],
fwhm0[good],
marker='o',
alpha=0.5,
mec='none',
mfc='b',
linestyle='none',
zorder=2)
ax0[row].get_yaxis().set_tick_params(which='both',
right=True,
width=1,
direction='in')
ax0[row].get_xaxis().set_tick_params(which='both',
top=True,
width=1,
direction='in')
# Compute average line profile from stack0_shift
# Later + on 10/03/2017
avg_stack = np.average(stack0_shift, axis=0)
x0_avg = np.arange(-25, 25)
if row == 0: axi = fig.add_axes([0.60, 0.81, 0.25, 0.15])
if row == 1: axi = fig.add_axes([0.60, 0.36, 0.25, 0.15])
axi.plot(x0_avg * pscale, avg_stack, 'k-')
axi.set_ylim([-0.4, 1.1])
axi.set_xlim([-2.0, 2.0])
axi.set_xticks(range(-2, 2, 1))
axi.set_xlabel('X [arcsec]', fontsize=8)
axi.tick_params(labelsize=8)
axi.minorticks_on()
p0 = [0.0, 1.0, 0.0, 2.0]
try:
popt, pcov = curve_fit(gauss1d, x0_avg, avg_stack, p0=p0)
fit_good = 1
except ValueError:
print len(np.where(np.isnan(x0_avg))[0])
print len(np.where(np.isnan(avg_stack))[0])
fit_good = 0
if fit_good:
avg_fwhm0 = popt[3] * 2 * np.sqrt(2 * np.log(2)) * pscale
avg_fwhm_Z = avg_fwhm0 / airmass**0.6 # + on 18/04/2018
axi.plot(x0_avg * pscale, gauss1d(x0_avg, *popt), 'r--')
axi.annotate('FWHM = %.3f" (%.3f")' %
(avg_fwhm0, avg_fwhm_Z), [0.50, 0.025],
xycoords='axes fraction',
ha='center',
va='bottom',
fontsize=8)
ax0[row].axhline(y=avg_fwhm0,
linewidth=2,
color='r',
linestyle='--',
zorder=1)
# Median FWHM | Later + on 10/03/2017
med_fwhm0 = np.median(fwhm0[good])
med_fwhm0_Z = med_fwhm0 / airmass**0.6 # + on 18/04/2018
ax0[row].axhline(y=med_fwhm0,
linewidth=2,
color='g',
linestyle='--',
zorder=1)
# Axes labeling
ax0[row].set_ylabel('FWHM [arcsec]')
if row == 1 or nn == n_files - 1:
ax0[row].set_xlabel('Y [pixel]')
else:
ax0[row].set_xticklabels([])
if nn == n_files - 1:
if row == 0:
ax0[row + 1].axis('off')
# Annotation
txt0 = files[nn] + '\nTarget: ' + hdr0[
'OBJECT'] #.split(' ')[0]
ax0[row].annotate(txt0, [0.025, 0.95],
xycoords='axes fraction',
ha='left',
va='top')
# + on 19/04/2018
ax0[row].annotate('AM = %.3f' % airmass, [0.025, 0.025],
xycoords='axes fraction',
ha='left',
va='bottom')
# Later + on 10/03/2017
if check_quality:
req = hdr0['REQIQ'].replace('-percentile', '%')
raw = hdr0['RAWIQ'].replace('-percentile', '%')
i_raw = [
ii for ii in range(len(FWHM_IQ_C))
if raw in FWHM_IQ_C[ii]
][0]
i_req = [
ii for ii in range(len(FWHM_IQ_C))
if raw in FWHM_IQ_C[ii]
][0]
txt0 = 'Req. IQ: %s [%.2f"]\n' % (req, FWHM_IQ_J[i_req])
txt0 += 'Raw IQ: %s [%.2f"]\n' % (raw, FWHM_IQ_J[i_raw])
# Mod on 18/04/2018
if med_fwhm0_Z <= FWHM_IQ_J[i_raw]:
txt0 += 'PASS'
FWHM_med_QA[nn] = 'PASS' # + on 19/05/2018
else:
if med_fwhm0_Z <= FWHM_IQ_J[i_raw] * 1.25:
txt0 += 'USABLE'
FWHM_med_QA[nn] = 'USABLE' # + on 19/05/2018
if med_fwhm0_Z > FWHM_IQ_J[i_raw] * 1.25:
txt0 += 'FAIL'
FWHM_med_QA[nn] = 'FAIL' # + on 19/05/2018
# + on 19/05/2018
if fit_good:
if avg_fwhm_Z <= FWHM_IQ_J[i_raw]:
FWHM_avg_QA[nn] = 'PASS'
else:
if avg_fwhm_Z <= FWHM_IQ_J[i_raw] * 1.25:
FWHM_avg_QA[nn] = 'USABLE'
if avg_fwhm_Z > FWHM_IQ_J[i_raw] * 1.25:
FWHM_avg_QA[nn] = 'FAIL'
ax0[row].annotate(txt0, [0.975, 0.05],
ha='right',
xycoords='axes fraction',
va='bottom')
# Aesthetics
ax0[row].set_xlim([0, 1050])
if max(fwhm0[good]) > 3:
ax0[row].set_ylim([0, 3.0])
else:
ax0[row].set_ylim([min(fwhm0) - 0.025, max(fwhm0) + 0.075])
ax0[row].minorticks_on()
# + on 18/04/2018
ax2 = ax0[row].twinx()
ax2.set_ylabel(r"FWHM @ Zenith [arcsec]")
ax2.set_ylim(np.array(ax0[row].get_ylim()) / airmass**0.6)
ax2.minorticks_on()
if row != 1:
ax2.set_xticklabels([])
if row == 1 or nn == n_files - 1:
subplots_adjust(left=0.11,
bottom=0.10,
top=0.975,
right=0.875,
wspace=0.03,
hspace=0.05)
fig.savefig(pp, format='pdf')
# + on 14/05/2018
if fit_good:
FWHM_avg_arr[nn] = avg_fwhm0
FWHM_avg_arr_Z[nn] = avg_fwhm_Z
FWHM_med_arr[nn] = med_fwhm0
FWHM_med_arr_Z[nn] = med_fwhm0_Z
#endfor
if silent == False: mylogger.info('Writing : ' + out_pdf)
pp.close()
# + on 14/05/2018
fwhm_out_file = out_pdf.replace('.pdf', '.tbl')
arr0 = [
files, FWHM_avg_arr, FWHM_avg_arr_Z, FWHM_med_arr,
FWHM_med_arr_Z, FWHM_avg_QA, FWHM_med_QA
] # Mod on 19/05/2018
names0 = ('files', 'FWHM_avg', 'FWHM_avg_Z', 'FWHM_med',
'FWHM_med_Z', 'FWHM_avg_QA', 'FWHM_med_QA'
) # Mod on 19/05/2018
tab0 = Table(arr0, names=names0)
if silent == False: mylogger.info('Writing : ' + fwhm_out_file)
asc.write(tab0,
fwhm_out_file,
format='fixed_width_two_line',
overwrite=True)
out_pdf = out_pdf_default
#endelse
#endfor
if silent == False: mylogger.info('### End main : ' + systime())
def main(silent=False, verbose=True):
'''
Main function to plot trends of peak flows
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 2 August 2018
'''
if silent == False: log.info('### Begin main : '+systime())
main_file = '/Users/cly/Dropbox/Documents/Personals/Peak_Flows.xls'
data = read_excel(main_file)
dates = data['Date'].values
time = data['Time'].values
comm0 = data['Notes'].values
v1 = data['PF #1'].values
v2 = data['PF #2'].values
v3 = data['PF #3'].values
val = [v1, v2, v3]
avg_pf = np.average(val, axis=0)
high_el = np.array([xx for xx in range(len(data)) if
'8500' in str(comm0[xx])])
tucson = np.array([xx for xx in range(len(data)) if
'Tucson' in str(comm0[xx])])
travel = np.array([xx for xx in range(len(data)) if
'Travel' in str(comm0[xx])])
sick = np.array([xx for xx in range(len(data)) if
'sick' in str(comm0[xx]) or 'Sick' in str(comm0[xx])])
# data.Date = to_datetime(data['Date'], format='%Y-%m-%d %H:%M:%S.%f')
# data.set_index(['Date'],inplace=True)
fig, ax = plt.subplots(nrows=2)
ax[0].scatter(dates[high_el], avg_pf[high_el], edgecolor='none',
facecolor='red', alpha=0.5, label='Mt Hopkins (8500 ft)')
ax[0].scatter(dates[tucson], avg_pf[tucson], edgecolor='none',
facecolor='blue', alpha=0.5, label='Tucson (2500 ft)')
ax[0].scatter(dates[travel], avg_pf[travel], edgecolor='none',
facecolor='green', alpha=0.5, label='Travel')
ax[0].scatter(dates[sick], avg_pf[sick], 30, marker='x', color='red',
label='Sick')
#data['Date'], data['PF #1'])
#data.plot('Date', 'PF #1') #, xlim=[2016,2019])
ax[0].legend(loc='lower right', fontsize=10)
ax[1].scatter(time, avg_pf)
if silent == False: log.info('### End main : '+systime())
def main(field='',
dr='pdr1',
noOII=False,
DEIMOS=False,
Hecto=False,
Bino=False,
silent=False,
verbose=True):
'''
Main function to plot RA and Dec for each sub-sample of NB excess emitters
Parameters
----------
field : str
Name of field to read in. Either 'udeep' or 'deep'
dr : str
Data release name. Default: 'pdr1'
noOII : boolean
Indicate whether to NOT plot [OII] emitters. Default: False
DEIMOS : boolean
Indicate whether to plot Keck/DEIMOS FoV on PDF plots
Hecto : boolean
Indicate whether to plot MMT/Hecto FoV on PDF plots
Bino : boolean
Indicate whether to plot MMT/Bino FoV on PDF plots
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 28 February 2018
- Import subsample module to get NB excess emitter subsamples
- Call subsample to get galaxy field, [gal_field]
- Construct for loop to look over each galaxy field and subsample
- Define output PDF path
- Plot ra and dec for each galaxy field and NB subsamples
Modified by Chun Ly, 1 March 2018
- Add noOII keyword to prevent [OII] emitters from being plotted
- log.info output PDF file
- Add DEIMOS boolean keyword input and plot DEIMOS FoV when set
- Set axes limit for RA and Dec for each galaxy field
- ax.legend() visibility improvement, RA/Dec limit changes
- Bug fix: Placement of n_subsample for ax.legend() ncol determination
- Add Hecto boolean keyword input and plot Hecto FoV when set
- Update call to subsample.main(); simplify code
Modified by Chun Ly, 2 March 2018
- Call paths module to get path
Modified by Chun Ly, 3 March 2018
- Read in field coordinate file for specific FoV overlay
- Generate DEIMOS coordinate list, pass to plot_deimos_fov()
- Bug fix: Call plot_deimos_fov() outside of for loop
- List comprehension: require DEIMOS pointing inside field
- If statement before calling plot_deimos_fov()
- Get vertices from plot_deimos_fov()
Modified by Chun Ly, 4 March 2018
- Call in_deimos_field()
- Create table of targets in DEIMOS field, deimos_tab0
Modified by Chun Ly, 5 March 2018
- Write table of targets in DEIMOS field to LaTeX files
- Include RA, Dec, PA in DEIMOS target field table
- Simplify fld_arr0 cmd for exec
- Define and pass maskno into plot_deimos_fov()
Modified by Chun Ly, 7 March 2018
- Get average RA and Dec for fields
Modified by Chun Ly, 16 March 2018
- Overlay Hecto pointings from input coordinate list
- Hecto sub-code tested. Bug fix: f_idx -> h_idx
Modified by Chun Ly, 19 March 2018
- Read in PRIMUS catalog; Call overlay_primus()
Modified by Chun Ly, 20 March 2018
- Import and call ds9_mask_overlay() to overlay ds9 regions
Modified by Chun Ly, 21 March 2018
- Add Bino boolean keyword and plot Binospec FoV when set
- Change out_pdf suffix for Bino and Hecto case
- List comprehensions for mask/config centers
- Call subsample_in_pointing for DEIMOS fields
- Call subsample_in_pointing for Hecto fields
Modified by Chun Ly, 22 March 2018
- Call in_bino_field()
- Call subsample_in_pointing for Bino fields
'''
if silent == False: log.info('### Begin main : ' + systime())
if field == '':
log.warn("### [field] input not specified!!!")
log.warn("### Either 'udeep' or 'deep'")
log.warn('### Exiting!!!')
return
dir0 = paths.gdrive() # Mod on 02/03/2018
# + on 03/03/2018
if DEIMOS or Hecto or Bino:
field_coord_file = dir0 + 'field_coordinates.txt'
if silent == False: log.info('### Writing : ' + field_coord_file)
ptg_tab = asc.read(field_coord_file)
# + on 19/03/2018
PRIMUS_cat_file = dir0 + 'catalogs/primus/PRIMUS_mask_centers.txt'
PRIMUS_tab0 = asc.read(PRIMUS_cat_file)
tab0 = read_catalog.main(field=field,
dr=dr,
silent=silent,
verbose=verbose)
ra0, dec0 = tab0['ra'], tab0['dec']
# Mod on 01/03/2018
sub_dict0, gal_dict0 = subsample.main(tab0=tab0, field=field, dr=dr)
gal_field0 = gal_dict0.keys() # Unique galaxy field list
RA_lim_dict0 = {
'UD-COSMOS': [149.25, 151.00],
'UD-SXDS': [33.70, 35.45],
'D-COSMOS': [148.75, 151.80],
'D-DEEP2_3': [350.20, 353.95],
'D-ELAIS_N1': [240.10, 245.40]
}
DE_lim_dict0 = {
'UD-COSMOS': [1.30, 3.00],
'UD-SXDS': [-5.80, -4.10],
'D-COSMOS': [2.00, 3.75],
'D-DEEP2_3': [-1.90, 1.10],
'D-ELAIS_N1': [52.90, 56.85]
}
for t_field in gal_field0:
f_idx = gal_dict0[t_field] # Mod on 01/03/2018
# + on 07/03/2018
RA_avg = np.average(ra0[f_idx])
DE_avg = np.average(dec0[f_idx])
print 'RA/DE avg : ', t_field, RA_avg, DE_avg
fig, ax = plt.subplots()
n_subsample = 0
for key in sub_dict0.keys(): # Mod on 01/03/2018
s_idx = sub_dict0[key]
# Get the intersection of f_idx and s_idx
t_idx = list(set(f_idx) & set(s_idx))
print t_field, key, len(t_idx)
if len(t_idx) > 0:
m0 = 'o' if 'NB0921' in key else '+' if 'NB0816' in key else ''
c0 = 'red' if 'Ha' in key else 'green' if 'OIII' in key \
else 'blue'
t_name = key.replace('NB0', 'NB')
t_name = t_name.replace('OIII_', '[OIII] ')
t_name = t_name.replace('OII_', '[OII] ')
t_name = t_name.replace('Ha_', r'H$\alpha$ ')
t_name += ' (' + str(len(t_idx)) + ')'
# Mod on 01/03/2018
if (noOII and 'OII_' in key):
if silent == False: log.warn('## Will not plot ' + key)
else:
n_subsample += 1
ax.scatter(ra0[t_idx],
dec0[t_idx],
s=5,
marker=m0,
color=c0,
linewidth=0.5,
edgecolor='none',
alpha=0.5,
label=t_name)
#endif
#endfor
ax.set_xlabel('Right Ascension (deg)')
ax.set_ylabel('Declination (deg)')
ax.set_xlim([RA_lim_dict0[t_field][1], RA_lim_dict0[t_field][0]])
ax.set_ylim(DE_lim_dict0[t_field])
ax.annotate(t_field, [0.025, 0.975],
xycoords='axes fraction',
fontsize=12,
fontweight='bold',
ha='left',
va='top')
ax.minorticks_on()
# Mod on 01/03/2018
ncol = 3 if n_subsample % 3 == 0 else 2
ax.legend(loc='lower center',
ncol=ncol,
frameon=False,
fontsize=10,
framealpha=0.9)
# Overlay PRIMUS pointings | + on 19/03/2018
ax = overlay_primus(PRIMUS_tab0, ax)
# Overlay ds9 masked regions | + on 20/03/2018
tmp_field = t_field.split('-')[-1].replace('_', '-')
prefix = 'mask_dr1_s15b_' + field + '_NB0921_' + tmp_field + '*.reg'
ds9_file = glob.glob(dir0 + 'catalogs/masks_Hayashi+17/' + prefix)[0]
if silent == False: log.info('## ds9_file : ' + ds9_file)
ds9_mask_overlay.main(ax, ds9_file, color='black', alpha=0.15)
# Overlay DEIMOS FoV | + on 01/03/2018, Mod on 03/03/2018
if DEIMOS:
d_idx = [
xx for xx in range(len(ptg_tab))
if ((ptg_tab['Instr'][xx] == 'DEIMOS') and (
ptg_tab['Field'][xx] == t_field))
]
if len(d_idx) > 0:
t_tab = ptg_tab[d_idx]
pa = t_tab['PA'].data
a_coord = [[ra, de]
for ra, de in zip(t_tab['RA'], t_tab['Dec'])]
# Mod on 05/03/2018
maskno = [
mname.replace(t_field + '-D', '')
for mname in t_tab['MaskName']
]
ax, deimos_verts0 = plot_deimos_fov(ax, a_coord, maskno, pa=pa)
# + on 04/03/2018
deimos_fld_idx = in_deimos_field(tab0,
deimos_verts0,
silent=silent,
verbose=verbose)
# Get subsample sizes in each DEIMOS pointing | + on 04/03/2018
# Mod on 21/03/2018
deimos_outfile = dir0 + 'catalogs/' + t_field + '_deimos.tex'
ss_in_ptg(sub_dict0,
deimos_fld_idx,
t_tab,
'DEIMOS',
deimos_outfile,
silent=silent,
verbose=verbose)
#endif
#endif
# Overlay Hecto FoV | + on 01/03/2018, Mod on 16/03/2018
if Hecto:
h_idx = [
xx for xx in range(len(ptg_tab))
if ((ptg_tab['Instr'][xx] == 'Hecto') and (
ptg_tab['Field'][xx] == t_field))
]
if len(h_idx) > 0:
t_tab = ptg_tab[h_idx]
a_coord = [[ra, de]
for ra, de in zip(t_tab['RA'], t_tab['Dec'])]
configno = [
cname.replace(t_field + '-H', '')
for cname in t_tab['MaskName'].data
]
ax = plot_hecto_fov(ax, a_coord, configno)
hecto_fld_idx = in_hecto_field(tab0,
a_coord,
silent=silent,
verbose=verbose)
# Get subsample sizes in each Hecto pointing | Mod on 21/03/2018
hecto_outfile = dir0 + 'catalogs/' + t_field + '_hecto.tex'
ss_in_ptg(sub_dict0,
hecto_fld_idx,
t_tab,
'Hecto',
hecto_outfile,
silent=silent,
verbose=verbose)
#endif
#endif
# Overlay Binospec FoV | + on 21/03/2018
if Bino:
b_idx = [
xx for xx in range(len(ptg_tab))
if ((ptg_tab['Instr'][xx] == 'Bino') and (
ptg_tab['Field'][xx] == t_field))
]
if len(b_idx) > 0:
t_tab = ptg_tab[b_idx]
pa = t_tab['PA'].data
a_coord = [[ra, de]
for ra, de in zip(t_tab['RA'], t_tab['Dec'])]
maskno = [
mname.replace(t_field + '-B', '')
for mname in t_tab['MaskName'].data
]
ax, bino_verts0 = plot_bino_fov(ax, a_coord, maskno, pa=pa)
# + on 22/03/2018
bino_fld_idx = in_bino_field(tab0,
bino_verts0,
silent=silent,
verbose=verbose)
# Get subsample sizes in each Bino pointing | + on 22/03/2018
bino_outfile = dir0 + 'catalogs/' + t_field + '_bino.tex'
ss_in_ptg(sub_dict0,
bino_fld_idx,
t_tab,
'Bino',
bino_outfile,
silent=silent,
verbose=verbose)
#endif
#endif
# Mod on 01/03/2018
out_pdf = dir0 + 'plots/' + t_field + '_radec.pdf'
if noOII: out_pdf = out_pdf.replace('.pdf', '.noOII.pdf')
if DEIMOS: out_pdf = out_pdf.replace('.pdf', '.DEIMOS.pdf')
# Mod on 21/03/2018
if Hecto and Bino:
out_pdf = out_pdf.replace('.pdf', '.MMT.pdf')
else:
if Hecto: out_pdf = out_pdf.replace('.pdf', '.Hecto.pdf')
if Bino: out_pdf = out_pdf.replace('.pdf', '.Bino.pdf')
if silent == False: log.info('## Writing : ' + out_pdf)
fig.savefig(out_pdf, bbox_inches='tight')
if silent == False: log.info('### End main : ' + systime())
def run(path0, clean_file='', out_script='', silent=False, verbose=True,
overwrite=False):
'''
Create a .sh script to run cleanir.py for a set of files
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
overwrite : boolean
Overwrite files if they exists. Default: False
Returns
-------
Notes
-----
Created by Chun Ly, 7 March 2017
Modified by Chun Ly, 15 May 2017
- Call dir_check.main() to handle multiple date directories
Modified by Chun Ly, 30 May 2017
- Added overwrite option. Default is to not overwrite .sh files
- Fix bug when only one file is found
Modified by Chun Ly, 18 June 2017
- Fix to work with no date directory
Modified by Chun Ly, 22 January 2018
- Import glog and call for stdout and ASCII logging
- Pass mylogger to dir_check.main()
Modified by Chun Ly, 20 April 2018
- Change afq to rfq - row filtering generally produces better results
'''
logfile = path0+'cleanir_script.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin run : '+systime())
if clean_file == '': clean_file = 'clean.lis'
# + on 15/05/2017
dir_list, list_path = dir_check.main(path0, mylogger=mylogger, silent=silent,
verbose=verbose)
# Mod on 15/05/2017
for date,path in zip(dir_list,list_path):
clean_file0 = path+clean_file
if not exists(clean_file0):
mylogger.warn('File does not exist!!!')
mylogger.warn(clean_file0)
else:
if silent == False: mylogger.info('Reading : '+clean_file0)
files = np.loadtxt(clean_file0, dtype=type(str)).tolist()
if type(files) == str: files = [files] # Bug fix. Mod on 30/05/2017
out_script0 = path+'run_cleanir.sh' if out_script == '' \
else out_script
if date != '': # Mod on 18/06/2017
out_script0 = out_script0.replace('.sh', '.'+date+'.sh')
# Mod on 30/05/2017
if overwrite == False and exists(out_script0):
log.warn('## File found!!! : '+out_script0)
log.warn('## Will not overwrite!!!')
else:
if silent == False:
stat0 = 'Overwriting' if exists(out_script0) else 'Writing'
mylogger.info(stat0+' : '+out_script0)
f = open(out_script0, 'w')
for ii in xrange(len(files)):
cmd1 = cmd0+' -rfqo '+path+'c'+files[ii]+' '+path+files[ii]
f.write(cmd1+'\n')
f.close()
#endelse
#endelse
#endfor
if silent == False: mylogger.info('End run : '+systime())
def check_extended(h0, s_cat, seqno, return_irsa_cat=False, silent=False,
verbose=True):
'''
Query the 2MASS extended source catalog (XSC) to identify contamination
from extended sources
Parameters
----------
s_cat : astropy.table.Table
Astropy-formatted table
hd0 : FITS header
FITS header containing WCS to determine RA/Dec
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 27 February 2017
Modified by Chun Ly, 28 February 2017
- Include extended galaxies slightly outside of MMTCam FoV
- Use elliptical formula to determine if inside extended source
'''
if silent == False: log.info('### Begin check_extended: '+systime())
size0 = 1.25*h0['NAXIS1'] * pscale # Size of region to search
c0 = coords.SkyCoord(ra=h0['CRVAL1'], dec=h0['CRVAL2'], unit=u.deg)
i_cat0 = IRSA.query_region(c0, catalog='fp_xsc', spatial='Box',
width=size0)
flag_ext = np.zeros(len(s_cat)) # + on 28/02/2017
# Check if daofind sources are within elliptical region of extended sources
# + on 28/02/2017
if len(i_cat0) == 0:
log.info('No extended source found for : '+seqno)
else:
log.info('Extended sources found for : '+seqno)
if verbose == True: print i_cat0
w0 = WCS(h0)
sRA, sDec = w0.wcs_pix2world(s_cat['xcentroid'], s_cat['ycentroid'], 1)
sc = coords.SkyCoord(ra=sRA, dec=sDec, unit=u.deg)
for cc in range(len(i_cat0)):
ic = coords.SkyCoord(ra=i_cat0['clon'][cc], dec=i_cat0['clat'][cc],
unit=(u.hour, u.deg))
#dist0 = ic.separation(sc).to(u.arcsec).value
dra = (ic.ra.deg - sRA)*3600.0 * np.cos(np.radians(ic.dec.deg))
ddec = (ic.dec.deg - sDec)*3600.0
ang0 = np.radians(90.0-i_cat0['sup_phi'])
maj0 = i_cat0['r_k20fe'][cc]
min0 = maj0*i_cat0['sup_ba'][cc]
dist0 = ((dra*np.cos(ang0) + ddec*np.sin(ang0))/maj0)**2 + \
((dra*np.sin(ang0) - ddec*np.cos(ang0))/min0)**2
ext0 = np.where(dist0 <= 1.0)[0]
flag_ext[ext0] = 1
# print s_cat[ext0]
if silent == False: log.info('### End check_extended: '+systime())
if return_irsa_cat == False:
return flag_ext
else: flag_ext, i_cat0
def main(silent=False, verbose=True):
'''
Main function to derive errors from NB photometry
Parameters
----------
filter : str
Name of filter: 'NB704', 'NB711', 'NB816', 'NB921', 'NB973'
NB : array
NB magnitudes on AB system
sig_NB : array
error on [NB]
excess : array
BB - NB color on AB system
sig_excess : array
error on [excess]
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
flux
sig_flux
EW
sig_EW
Notes
-----
Created by Chun Ly, 13 December 2018
'''
if silent == False: log.info('### Begin main : ' + systime())
#Limiting magnitudes
m_NB = np.array([
26.7134 - 0.047, 26.0684, 26.9016 + 0.057, 26.7894 + 0.041,
27.3928 + 0.032, 26.7088 - 0.109, 25.6917 - 0.051
])
m_BB1 = np.array(
[28.0829, 28.0829, 27.7568, 27.8933, 28.0829, 26.8250, 26.8250])
m_BB2 = np.array(
[27.7568, 27.7568, 26.8250, 28.0829, 27.7568, 00.0000, 00.0000])
cont_lim = mag_combine(m_BB1, m_BB2, epsilon)
limit_dict = {'m_NB': m_NB, 'm_BB': cont_lim}
tab0, infile = get_data()
tab0 = get_errors(tab0,
filt_dict0,
BB_filt,
epsilon,
limit_dict=limit_dict)
outfile = infile.replace('.fits', '.errors.fits')
tab0.write(outfile, format='fits', overwrite=True)
plot_errors('Ha', filt_ref, tab0, limit_dict)
plot_flux_ew_errors('Ha', filt_ref, tab0)
if silent == False: log.info('### End main : ' + systime())
def check_prefix(final_prefix, input_lis, list_path='', path='',
mylogger=None, prereq=False, silent=False, verbose=True):
'''
Check if specific files from an input list exist with given prefix
Parameters
----------
final_prefix : str
Files with specific prefix to search for ('rnc', etc).
This will be added before the filenames in [input_lis]
input_lis : str
Filename for input list to check ('arc.lis', 'flat.lis', etc.)
If full path is included, do not provide [list_path]
list_path : str (Optional)
Full path for input_lis of it does not contain full path.
Must include '/' at the end
path : str (Optional)
Full path to individual files if [input_lis] contents do not contain
full path. Must include '/' at the end
prereq: boolean
Set if you're checking if necessary intermediate/input files are
available. If set and files exist, returns do_run = 1.
Default: False
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
do_run : int
0 - Not all files available
1 - All files available
Notes
-----
Created by Chun Ly, 5 May 2017
Modified by Chun Ly, 16 May 2017
- Switch path to an optional keyword
Modified by Chun Ly, 2 June 2017
- Changed path -> list_path for input_lis
- path is now for individual frames from the input_lis
Modified by Chun Ly, 18 December 2017
- Implement glog logging, allow mylogger keyword input
Modified by Chun Ly, 25 June 2018
- Add prereq keyword option to check if intermediate files are available
'''
# + on 18/12/2017
if type(mylogger) == type(None):
mylog, clog = 0, log
else:
mylog, clog = 1, mylogger
if silent == False: clog.info('### Begin check_prefix : '+systime())
input_lis0 = list_path+input_lis
if silent == False: clog.info('Reading : '+input_lis0) # Mod on 18/12/2017
files = np.loadtxt(input_lis0, dtype=type(str))
f_exist = [file0 for file0 in files if
exists(path+final_prefix+file0) == True]
f_noexist = [file0 for file0 in files if
exists(path+final_prefix+file0) == False]
do_run = 0
# Mod on 25/06/2018
if not prereq:
if len(f_exist) == 0:
clog.info('No files exist, as expected') # Mod on 18/12/2017
do_run = 1
else:
# Mod on 18/12/2017
if len(f_exist) != len(files):
clog.warn('Some files do not exist!')
clog.warn(', '.join(f_noexist))
else:
clog.info('All files exist!!!')
else:
if len(f_exist) == 0:
clog.warn('Intermediate files unavailable!!')
else:
clog.info('Intermediate files available')
do_run = 1
if silent == False: clog.info('End check_prefix : '+systime())
return do_run
def main(silent=False, verbose=True):
'''
Main function to read in Starburst99 models and compute UV lum
Parameters
----------
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 16 June 2019
'''
if silent == False: log.info('### Begin main : ' + systime())
Z = [0.05, 0.02, 0.008, 0.004, 0.0004]
Z = np.array(Z)
Llambda = np.array([40.12892, 40.21840, 40.25546, 40.27597, 40.30982])
'''
From Starburst99 CSF 1 Msun/yr model with Kroupa IMF and
Padova stellar tracks. Log units of erg/s/Ang. Using
age of 0.3E9 (except 0.1E9 for 2.5xZ_solar)
'''
lambda0 = 1500.0 * u.Angstrom
fig, ax = plt.subplots(ncols=2, nrows=2)
# nuL_nu in ax[0][0]
# nu Lnu = lambda Llambda
nuLnu = Llambda + np.log10(lambda0.value)
ylabel = r'$\nu L_{\nu}(1500\AA)$/SFR [erg s$^{-1}$/$M_{\odot}$ yr$^{-1}$]'
nuLnu_fit_kr, nuLnu_fit_ch = plot_panel(ax[0][0],
Z,
nuLnu,
ylabel,
showlegend=True)
# L_nu in ax[0][1]
nu_offset = np.log10(c0.to(u.m / u.s).value / lambda0.to(u.m).value)
Lnu = nuLnu - nu_offset
ylabel = r'$L_{\nu}(1500\AA)$/SFR [erg s$^{-1}$ Hz$^{-1}$/$M_{\odot}$ yr$^{-1}$]'
Lnu_fit_kr, Lnu_fit_ch = plot_panel(ax[0][1], Z, Lnu, ylabel)
# Plot K98 relation
ax[0][1].scatter([1.0],
-1 * np.log10(1.4e-28),
color='green',
marker='o',
s=50,
edgecolor='none',
alpha=0.5)
ax[0][1].annotate('K98', [1.05, -1 * np.log10(1.4e-28 * 0.98)],
xycoords='data',
fontsize=8,
ha='left',
va='bottom')
# Plot H-alpha in ax[1][0]
LHa = np.array([41.061, 41.257, 41.381, 41.439, 41.536])
ylabel = r'$L({\rm H}\alpha)$/SFR [erg s$^{-1}$/$M_{\odot}$ yr$^{-1}$]'
LHa_fit_kr, LHa_fit_ch = plot_panel(ax[1][0], Z, LHa, ylabel, labelx=True)
# Plot nuLnu vs LHa in ax[1][1]
ylabel = r'$\nu L_{\nu}(1500\AA)/L({\rm H}\alpha)$'
nuLnu_LHa_fit_kr, \
nuLnu_LHa_fit_ch = plot_panel(ax[1][1], Z, nuLnu-LHa, ylabel,
labelx=True)
plt.subplots_adjust(left=0.085,
right=0.995,
bottom=0.07,
top=0.98,
wspace=0.225,
hspace=0.04)
out_pdf = '/Users/cly/Google Drive/NASA_Summer2015/Plots/sfr_metallicity_plot.pdf'
fig.set_size_inches(10, 8)
fig.savefig(out_pdf)
out_npzfile = out_pdf.replace('.pdf', '_fit.npz')
np.savez(out_npzfile,
nuLnu_fit_kr=nuLnu_fit_kr,
nuLnu_fit_ch=nuLnu_fit_ch,
Lnu_fit_kr=Lnu_fit_kr,
Lnu_fit_ch=Lnu_fit_ch,
LHa_fit_kr=LHa_fit_kr,
LHa_fit_ch=LHa_fit_ch,
nuLnu_LHa_fit_kr=nuLnu_LHa_fit_kr,
nuLnu_LHa_fit_ch=nuLnu_LHa_fit_ch)
if silent == False: log.info('### End main : ' + systime())
def psf_contours(files=None, path0=None, out_pdf_plot=None, silent=False,
verbose=True):
'''
Generate contour plots for the MMTCam PSF
Parameters
----------
files : list
List of files
path0 : string
Path to files. If not provided it is assumed that [files] has the full
path name
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 24 February 2017
- Later mod to handle plotting styles
- Later Mod to include header info in annotation
- Use filled contours with plasma cmap
- Add colorbar
Modified by Chun Ly, 25 February 2017
- Add colorbar for last subplot
- Get FWHM and FWQM from fwhm_fwqm_image()
- Call opt.curve_fit() to fit 2-D Gaussians
- Overlay cyan contours for best 2-D fit
Modified by Chun Ly, 26 February 2017
- Minor stylistic plotting changes
- Call get_mst() to get MST time
- Draw center of best fit
- Call draw_NE_vector() function
Modified by Chun Ly, 26 February 2017
- Use cosmicray_median() to interpolate over CRs
- Use psf_im_cr over psf_im
- Use uniform_filter() to smooth data with a size of 3 pixels
Modified by Chun Ly, 01 March 2017
- Annotate plot with wind data
- Change x and y limit to give more room
'''
if files == None and path0 == None:
log.error('files and path0 keywords not provided')
log.error('Exiting!!!')
return
if silent == False: log.info('### Begin psf_contours: '+systime())
if files == None and path0 != None:
files, seqno = get_files(path0)
else:
if files != None: seqno = get_seqno(files)
post_dir0 = path0 + 'post/'
if out_pdf_plot == None: out_pdf_plot = path0+'psf_contours.pdf'
pp = PdfPages(out_pdf_plot)
ncols, nrows = 3, 3
n_files = len(files)
for ff in xrange(n_files):
psf_file = post_dir0+seqno[ff]+'.fits'
psf_im, h0 = fits.getdata(psf_file, header=True)
# Identify and interpolate over any extraneous CRs | + on 26/02/2017
psf_im_cr, mask = cosmicray_median(psf_im, thresh=5, rbox=11)
psf_im_cr /= np.max(psf_im_cr)
psf_im_sm = uniform_filter(psf_im_cr, size=3) # + on 26/02/2017
if ff == 0:
shape0 = psf_im_cr.shape
x0 = pscale*np.arange(-1*shape0[0]/2.0,shape0[0]/2.0)
y0 = pscale*np.arange(-1*shape0[1]/2.0,shape0[1]/2.0)
if ff % (ncols*nrows) == 0:
fig, ax = plt.subplots(nrows, ncols)
row, col = ff / ncols % nrows, ff % ncols
# Later mod on 24/02/2017, 26/02/2017
cf = ax[row,col].contourf(x0, y0, psf_im_sm, levels=c_levels,
cmap=plt.cm.plasma)
# Mod on 25/02/2017 to include colorbar for last subplot
# Mod on 26/02/2017 to shrink height
if col == ncols-1:
cax = fig.add_axes([0.925, 0.76-0.32*row, 0.01, 0.14])
if ff == n_files-1:
cax = fig.add_axes([0.605, 0.76-0.32*row, 0.01, 0.14])
if col == ncols-1 or ff == n_files-1:
cbar = fig.colorbar(cf, ax=ax[row,col], cax=cax)
cbar.ax.tick_params(labelsize=8)
if row == nrows-1:
ax[row,col].set_xlabel('X [arcsec]')
else:
if ((n_files-1)-ff) > ncols-1:
ax[row,col].set_xticklabels([])
if ff == n_files-1:
for cc in range(ncols): ax[row,cc].set_xlabel('X [arcsec]')
if col == 0:
ax[row,col].set_ylabel('Y [arcsec]')
else: ax[row,col].set_yticklabels([])
# Mod on 26/02/2017
t_label = seqno[ff]+'.'+h0['FILTER']
ax[row,col].annotate(t_label, [0.025,0.975], weight='bold', ha='left',
va='top', xycoords='axes fraction', fontsize=10)
t_nstack = r'N$_{\rm stack}$=%i' % h0['NBRIGHT']
ax[row,col].annotate(t_nstack, [0.975,0.975], weight='bold', ha='right',
va='top', xycoords='axes fraction', fontsize=10)
# Compute image quality | + on 25/02/2017
f_annot = 'UTC='+h0['UT']+' MST='+get_mst(h0)+'\n' # + on 26/02/2017
fwhm0, fwqm0 = fwhm_fwqm_size(psf_im_cr, pscale)
f_annot += 'Area: FWHM=%.2f", FWQM=%.2f"\n' % (fwhm0, fwqm0)
sigG = fwhm0/f_s/pscale.to(u.arcsec).value
ini_guess = (1.0, 25, 25, sigG, sigG, 0.0, 0.0)
gx = np.linspace(0,shape0[0]-1,shape0[0])
gy = np.linspace(0,shape0[1]-1,shape0[1])
gx, gy = np.meshgrid(gx, gy)
psf_im_re = psf_im_cr.reshape(shape0[0]*shape0[1])
popt, pcov = opt.curve_fit(gauss2d, (gx, gy), psf_im_re, p0=ini_guess)
FWHMx = popt[3] * f_s * pscale.to(u.arcsec).value
FWHMy = popt[4] * f_s * pscale.to(u.arcsec).value
f_annot += r'2DFit: FW$_1$=%.2f", FW$_2$=%.2f", ' % (FWHMx,FWHMy)
f_annot += r'$\theta$=%.2f' % np.degrees(popt[5]) + '\n'
# + on 01/03/2017
f_annot += 'Y1: avg=%.1f, max=%.1f, dir=%.1f\n' % (h0['Y1_AVG'],h0['Y1_MAX'],
h0['Y1_DIR'])
f_annot += 'Y2: avg=%.1f, max=%.1f, dir=%.1f' % (h0['Y2_AVG'],h0['Y2_MAX'],
h0['Y2_DIR'])
ax[row,col].set_xlim([-5,5])
ax[row,col].set_ylim([-5,5])
# Mod on 27/02/2017 to have a fill color
ax[row,col].annotate(f_annot, [0.025,0.915], xycoords='axes fraction',
ha='left', va='top', fontsize=8, zorder=10,
bbox=bbox_props)
# Overlay 0.25, 0.50, and 0.75 quartile contours for 2-D Gaussian fit
# + on 25/02/2017
f_data = gauss2d((gx, gy), *popt)
f_data /= np.max(f_data)
levels = np.array([0.25,0.5,0.75])
CS = ax[row,col].contour(x0, y0, f_data.reshape(shape0[0],shape0[1]),
colors='c', linewidth=2, cmap=None,
levels=levels.tolist())
if col==0: ax[row,col].clabel(CS, CS.levels, fmt='%.2f', inline=1,
inline_spacing=0.25, fontsize=8)
# Plot center of fit | + on 26/02/2017
xcen = v_pscale*(-1*shape0[0]/2.0+popt[1])
ycen = v_pscale*(-1*shape0[1]/2.0+popt[2])
ax[row,col].plot(xcen, ycen, 'o', mfc='c', mec='none', alpha=0.5)
hdr_annotate(h0, ax[row,col]) # + on 24/02/2017
draw_NE_vector(h0, ax[row,col]) # + on 26/02/2017
if ff == n_files-1:
for cc in range(col+1,ncols): ax[row,cc].axis('off')
for rr in range(row+1,nrows):
for cc in range(ncols): ax[rr,cc].axis('off')
if ff % (ncols*nrows) == ncols*nrows-1 or ff == n_files-1:
ax[0,1].set_title('MMTCam : '+path0.split('/')[-2], loc=u'center',
fontsize=14, weight='bold')
subplots_adjust(left=0.025, bottom=0.025, top=0.975, right=0.975,
wspace=0.02, hspace=0.02)
fig.set_size_inches(8,8)
fig.savefig(pp, format='pdf', bbox_inches='tight')
#endfor
pp.close()
if silent == False: log.info('### End psf_contours: '+systime())
def make_postage(files=None, path0=None, n_stack=5, size=50,
user='******', passwd='', silent=False, verbose=True):
'''
Create cut-outs and median stack to produce image of the
point-spread function
Parameters
----------
files : list
List of files
path0 : string
Path to files. If not provided it is assumed that [files] has the full
path name
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 23 February 2017
Modified by Chun Ly, 24 February 2017
- Include FITS header in cutout images
Modified by Chun Ly, 26 February 2017
- Use cosmicray_median() to interpolate over CRs
- Include number of stack sources in FITS header
Modified by Chun Ly, 28 February 2017
- Call query_mmtlog_wind() function
- Add user and passwd keyword to pass on
Modified by Chun Ly, 1 March 2017
- Check if wind data table is available before running query_mmtlog_wind()
- Call wind_avg_max() function
'''
if files == None and path0 == None:
log.error('files and path0 keywords not provided')
log.error('Exiting!!!')
return
if silent == False: log.info('### Begin make_postage: '+systime())
if files == None and path0 != None:
files, seqno = get_files(path0)
# path0 = None # Reset since files will have full path
else:
if files != None: seqno = get_seqno(files)
# Query for wind data | + on 28/02/2017
# Mod on 01/03/2017 to check if file exists
wind_file = path0+'wind_data.tbl'
if not exists(wind_file):
u_start = fits.getheader(files[0])['DATE-OBS']
u_stop = fits.getheader(files[-1])['DATE-OBS']
wind_tab0 = query_mmtlog_wind(u_start, u_stop, user=user,
passwd=passwd, path0=path0)
else:
if silent == False: log.info('### File found! Reading : '+wind_file)
wind_tab0 = asc.read(wind_file, format='fixed_width_two_line')
post_dir0 = path0 + 'post/'
if not exists(post_dir0):
if silent == False: log.info('Creating : '+post_dir0)
os.mkdir(post_dir0)
out_cat_dir0 = path0+out_cat_dir
for ff in xrange(len(files)):
basename = os.path.basename(files[ff])
image, hdr = fits.getdata(files[ff], header=True)
mean, median, std = sigma_clipped_stats(image, sigma=2.0, iters=5)
image_sub = image - median
in_cat = out_cat_dir0+basename.replace('.fits.gz','.tbl').\
replace('.fits','.tbl')
s_cat = asc.read(in_cat, format='fixed_width_two_line')
# Handle failure if only one source is available and is near edge
# + on 28/02/2017
not_edge = np.where((s_cat['xcentroid'] > 50.0) &
(s_cat['xcentroid'] <= hdr['NAXIS1']-50) &
(s_cat['ycentroid'] > 50.0) &
(s_cat['ycentroid'] <= hdr['NAXIS2']-50))[0]
s_cat = s_cat[not_edge]
# + on 28/02/2017
good = np.where(s_cat['peak'] >= 0.33*max(s_cat['peak']))[0]
s_cat = s_cat[good]
n_bright = np.min([n_stack,len(s_cat)])
bright = range(n_bright)
s_cat = s_cat[bright]
x0 = np.round_(s_cat['xcentroid'])
y0 = np.round_(s_cat['ycentroid'])
im0 = np.zeros( (len(bright), size, size) )
size2d = u.Quantity((size, size), u.pixel)
for ii in range(n_bright):
pos0 = (x0[ii], y0[ii])
cutout = Cutout2D(image_sub, pos0, size2d, mode='partial',
fill_value=np.nan)
# Identify and interpolate over CRs
cutout_cr, crmask = cosmicray_median(cutout.data, thresh=5, rbox=11)
im0[ii] = cutout_cr/np.max(cutout_cr)
out_fits = post_dir0+seqno[ff]+'.fits'
psf_im = np.nanmedian(im0, axis=0)
hdr.set('NBRIGHT', n_bright) # + on 26/02/2017
wind_avg_max(wind_tab0, hdr) # + on 01/03/2017
fits.writeto(out_fits, psf_im, hdr, overwrite=True)
if silent == False: log.info('### End make_postage: '+systime())
def main(path0, targets, outfile=None, silent=False, verbose=True):
'''
Generate ASCII file summarizing observations
Parameters
----------
path0 : str
Parent path for all files
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 25 April 2017
Modified by Chun Ly, 5 May 2017
- Handle overwriting file
Modified by Chun Ly, 3 June 2017
- Bug fix: Check if hdr_info.QA.tbl exists
'''
if silent == False: log.info('### Begin main : ' + systime())
Targets, ObsDate, ObsSet = [], [], []
TotalTime, gratwave, Airmass = [], [], []
TellStar, TellSet, TellAM = [], [], [] # Later Mod on 25/04/2017
for tt in range(len(targets)):
tt_path = path0 + targets[tt] + '/'
dir_list, list_path = dir_check.main(tt_path,
silent=True,
verbose=False)
cnt = 0
for path in list_path:
# Mod on 25/04/2017
txt = targets[tt] if cnt == 0 else '...'
Targets.append(txt) #targets[tt])
QA_file = path + '/hdr_info.QA.tbl'
# Mod on 03/06/2017
if not exists(QA_file):
log.warn('## File not found! ' + QA_file)
ObsDate.append('N/A')
gratwave.append('N/A')
ObsSet.append('N/A')
TotalTime.append('N/A')
Airmass.append('N/A')
TellStar.append('N/A')
TellSet.append('N/A')
TellAM.append('N/A')
else:
QA_tab = asc.read(QA_file, format='fixed_width_two_line')
# All science targets
idx = [
xx for xx in range(len(QA_tab))
if ('obj' in QA_tab['QA'][xx]) or (
'sky' in QA_tab['QA'][xx])
]
# Later Mod on 25/04/2017
tab_ref = QA_tab[idx][0]
t_date = tab_ref['UT_date'].split('T')[0]
exptime = tab_ref['exptime']
ObsDate.append(t_date)
gratwave.append(tab_ref['gratwave'])
ObsSet.append(str(len(idx)) + 'x' + str(exptime) + 's')
TotalTime.append('%.2f' % (len(idx) * exptime / 60.0))
AM0 = QA_tab['airmass'][idx]
Airmass.append('%.3f-%.3f' % (np.min(AM0), np.max(AM0)))
t_idx = [
xx for xx in range(len(QA_tab))
if ('telluric' in QA_tab['QA'][xx])
]
t_names = list(set(QA_tab['object'][t_idx]))
telstar, telset, telAM = get_telluric_info(
QA_tab, t_idx, t_names)
TellStar.append(telstar)
TellSet.append(telset)
TellAM.append(telAM) # Later + on 25/04/2017
cnt += 1
#endelse
#endfor
#endfor
arr0 = [
Targets, ObsDate, ObsSet, TotalTime, gratwave, Airmass, TellStar,
TellSet, TellAM
]
names0 = ('Name', 'UT_Date', 'Sequence', 'Int_Time', 'Grating_Wave',
'Airmass', 'Telluric_Star', 'Telluric_Seq', 'Telluric_AM')
tab0 = Table(arr0, names=names0)
print tab0
if outfile == None: outfile = path0 + 'obs_summary.txt'
# Mod on 06/05/2017
if silent == False:
stat0 = 'Overwriting : ' if exists(outfile) else 'Writing : '
log.info(stat0 + outfile)
asc.write(tab0,
output=outfile,
format='fixed_width_two_line',
overwrite=True)
if silent == False: log.info('### End main : ' + systime())
def main(rawdir, line_source='', mylogger=None, silent=False, verbose=True):
'''
Main function for wave_cal_script
Parameters
----------
rawdir : str
Path to raw files. Must end in a '/'
line_source : str
Type of lines to use for wavelength calibration. Option is
either 'arc' or 'OH
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 7-8 October 2017
Modified by Chun Ly, 8 November 2017
- Specify lampspec and outspec
Modified by Chun Ly, 16 November 2017
- Handle line_source == 'OH'
- Generalized arrays: arc -> frame
- Specify GNIRS log file
Modified by Chun Ly, 20 November 2017
- Bug fix: prefix needed for [frames] for line_source == OH
Modified by Chun Ly, 9 January 2018
- Import glog and call for stdout and ASCII logging
Modified by Chun Ly, 9 January 2018
- Allow mylogger keyword
Modified by Chun Ly, 30 May 2018
- Change order for nswavelength fitting
Modified by Chun Ly, 16 June 2018
- Change coordlist for OH skylines
Modified by Chun Ly, 19 June 2018
- Force function to legendre
- Set fwidth in nswavelength call to depend on slitwidth
Modified by Chun Ly, 21 June 2018
- Include ending print statement
Modified by Chun Ly, 10 July 2018
- Modify threshold for OH lines from 50 to 25
'''
# Mod on 10/01/2018
if type(mylogger) == type(None):
logfile = rawdir + 'QA_wave_cal.log'
mylogger = glog.log0(logfile)._get_logger()
if silent == False: mylogger.info('### Begin main : ' + systime())
timestamp = systime().replace(':', '.')
logfile = rawdir + 'gnirs_' + timestamp + '.log'
rawdir = check_path(rawdir)
if line_source == '':
mylogger.warn("Must specify line_source keyword: ")
mylogger.warn("line_source='arc' or line_source='OH'")
mylogger.warn("Exiting!!!")
return
else:
out_script = rawdir + 'wave_cal_' + line_source + '.py'
if silent == False: mylogger.info('Writing : ' + out_script)
f0 = open(out_script, 'w')
line0 = [
'iraf.gemini(_doprint=0)', 'iraf.gemini.gnirs(_doprint=0)',
'iraf.gemini.unlearn()', 'iraf.gemini.gemtools.unlearn()',
'iraf.gemini.gnirs.unlearn()', 'iraf.set(stdimage="imt4096")',
'iraf.gemini.nsheaders("gnirs")'
]
#'iraf.gemini.gnirs.logfile = "%s"' % logfile] # + on 16/11/2017
f0.writelines("\n".join(line0) + "\n")
if line_source == 'arc': frame_list = rawdir + 'arc.lis'
if line_source == 'OH': frame_list = rawdir + 'obj.OH.lis'
frames = np.loadtxt(frame_list, dtype=type(str))
if line_source == 'OH':
frames = ['rbnc' + file0 for file0 in frames]
frame_hdr = fits.getheader(rawdir + frames[0])
crpix = n_sp_pix / 2.0
crval = frame_hdr['gratwave'] * 1e4 # in Angstroms
if frame_hdr['FILTER2'] == 'X_G0518':
cdelt = -0.094 * 1e4 / n_sp_pix
if frame_hdr['FILTER2'] == 'J_G0517':
cdelt = -0.113 * 1e4 / n_sp_pix
mylogger.info('## CRVAL : %.1f ' % crval)
mylogger.info('## CDELT : %.1f CRPIX : %.1f' % (cdelt, crpix))
line1 = ['crval = %f' % crval, 'crpix = %f' % crpix, 'cdelt = %f' % cdelt]
f0.writelines("\n".join(line1) + "\n")
# Get slit length | + on 19/06/2018q
slitwidth = np.float(frame_hdr['SLIT'].split('arcsec')[0])
pscale = np.sqrt(frame_hdr['CD1_1']**2 +
frame_hdr['CD2_1']**2) * 3600.0 * u.arcsec
fwidth = 1.5 * slitwidth / pscale.to(u.arcsec).value
if line_source == 'arc':
coordlist = 'gnirs$data/argon.dat'
database = 'database/'
threshold = 50
if line_source == 'OH':
coordlist = rawdir + 'rousselot2000_convl.dat'
if not exists(coordlist):
log.warn('File does not exists!!! : ' + coordlist)
database = 'database_OH/'
threshold = 25
# Mod on 08/11/2017
line2 = [
"coordlist = '%s'" % coordlist,
"database = '%s'" % database,
"lampspec = '%s_stack.fits'" % line_source,
"outspec = 'w%s_stack.fits'" % line_source,
"threshold = %f" % threshold,
"logfile = '%s'" % logfile
] # + on 16/11/2017
f0.writelines("\n".join(line2) + "\n")
# Mod on 08/11/2017, 16/11/2017
cmd = "iraf.gnirs.nswavelength(lampspec, outprefix='',"+\
"outspectra=outspec, crval=crval, cdelt=cdelt, crpix=crpix, "+\
"coordlist=coordlist, database=database, fl_inter='yes', "+\
"function='legendre', cradius=20, threshold=threshold, "+\
"fwidth=%.1f, " % fwidth +"order=3, logfile=logfile)"
f0.write(cmd + '\n')
f0.write('print("Completed! Return to other terminal and hit RETURN")\n')
f0.close()
if silent == False: mylogger.info('### End main : ' + systime())
def find_stars(files=None, path0=None, plot=False, out_pdf_plot=None,
silent=False, verbose=True):
'''
Find stars in an image and return a catalog of positions
Parameters
----------
files : list
List of files
path0 : string
Directory path to files.
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
Notes
-----
Created by Chun Ly, 23 February 2017
- Later modified to plot images and overlay sources
- Adjust scale to using IRAF's zscale
- Call remove_dup_sources()
Modified by Chun Ly, 28 February 2017
- Call check_extended() to get flag indicating extended, flag_ext
'''
if silent == False: log.info('### Begin find_stars: '+systime())
if files == None and path0 == None:
log.error('files and path0 keywords not provided')
log.error('Exiting!!!')
return
if files == None and path0 != None:
files, seqno = get_files(path0)
# path0 = None # Reset since files will have full path
else:
if files != None: seqno = get_seqno(files)
# Later + on 23/02/2017
out_cat_dir0 = path0+out_cat_dir
if not exists(out_cat_dir0):
if silent == False: log.info('Creating : '+out_cat_dir0)
os.mkdir(out_cat_dir0)
s_date = path0.split('/')[-2] # Mod on 25/02/2017 for minor bug
if plot == True:
if out_pdf_plot == None:
out_pdf_plot = path0+'find_stars.pdf'
pp = PdfPages(out_pdf_plot)
for ff in xrange(len(files)): #[34,35,36,37,38,39]: #xrange(len(files)):
basename = os.path.basename(files[ff])
image, hdr = fits.getdata(files[ff], header=True)
mean, median, std = sigma_clipped_stats(image, sigma=2.0, iters=5)
image_sub = image - median
if verbose == True:
log.info('%s mean/med/sig: %f %f %f' %
(seqno[ff], mean, median, std))
#Later Mod on 23/02/2017 to lower threshold
daofind = DAOStarFinder(fwhm=8.0, threshold=5.*std)
s_cat = daofind(image_sub)
# Exclude saturated objects
unsat = np.where(s_cat['peak'] <= 60000.0)[0]
sat = np.where(s_cat['peak'] > 60000.0)[0]
cat_sat = s_cat[sat]
s_cat = s_cat[unsat]
s_cat.sort(['peak'])
s_cat.reverse()
# s_cat.pprint()
# + on 28/02/2017
flag_ext = check_extended(hdr, s_cat, seqno[ff], verbose=False)
i_extend = np.where(flag_ext == 1)[0]
i_point = np.where(flag_ext == 0)[0]
if len(i_extend) > 0:
cat_ext = s_cat[i_extend]
s_cat = s_cat[i_point]
#endif
# Later + on 23/02/2017
bad = remove_dup_sources(s_cat)
if len(bad) > 0:
cat_bad = s_cat[bad]
s_cat.remove_rows(bad)
if ff == 0 and silent == False: s_cat.pprint()
# + on 23/02/2017
out_cat = out_cat_dir0+basename.replace('.fits.gz','.tbl')
out_cat = out_cat.replace('.fits','.tbl')
s_cat.write(out_cat, format='ascii.fixed_width_two_line',
overwrite=True)
# Write extended catalog | + on 28/02/2017
if len(i_extend) >0:
out_cat_ext = out_cat.replace('.tbl','.ext.tbl')
cat_ext.write(out_cat_ext, format='ascii.fixed_width_two_line',
overwrite=True)
# Later + on 23/02/2017
if len(bad) >0 and verbose == True:
log.info('The following will be removed : ')
cat_bad.pprint()
if len(bad) >0:
out_cat_bad = out_cat.replace('.tbl','.bad.tbl')
cat_bad.write(out_cat_bad, format='ascii.fixed_width_two_line',
overwrite=True)
if plot == True:
pos0 = (s_cat['xcentroid'], s_cat['ycentroid'])
aper0 = CircularAperture(pos0, r=8.)
pos0 = (cat_sat['xcentroid'], cat_sat['ycentroid'])
sat_aper0 = CircularAperture(pos0, r=8.)
pos0 = (cat_bad['xcentroid'], cat_bad['ycentroid'])
bad_aper0 = CircularAperture(pos0, r=8.)
fig, ax = plt.subplots()
z1, z2 = zscale.get_limits(image_sub)
# print z1, z2
norm = ImageNormalize(vmin=z1, vmax=z2) #stretch=SqrtStretch())
ax.imshow(image_sub, cmap='Greys', origin='lower', norm=norm)
aper0.plot(color='blue', lw=1.5, alpha=0.5)
sat_aper0.plot(color='red', lw=1.5, alpha=0.5)
bad_aper0.plot(color='magenta', lw=1.5, alpha=0.5)
# Label bright sources | + on 28/02/2017
bright = np.where(s_cat['peak'] >= 0.33*max(s_cat['peak']))[0]
for nn in bright:
t_pos = [s_cat['xcentroid'][nn], s_cat['ycentroid'][nn]+10]
ax.annotate(str(nn+1), t_pos, xycoords='data', ha='center',
va='bottom', color='b', weight='medium')
# Mark sources excluded by extended criteria | + on 28/02/2017
if len(i_extend) > 0:
ax.plot(cat_ext['xcentroid'], cat_ext['ycentroid'], 'rx', linewidth=2)
t_ann = s_date+'/'+os.path.basename(files[ff])
ax.set_title(t_ann, loc=u'center', fontsize=14, weight='bold')
#ax.annotate(t_ann, [0.025,0.975], xycoords='axes fraction',
# ha='left', va='top', bbox=bbox_props)
ax.set_xlim([0,hdr['NAXIS1']])
ax.set_ylim([0,hdr['NAXIS2']])
ax.set_xlabel('X [pixels]')
ax.set_ylabel('Y [pixels]')
fig.set_size_inches(8,8)
fig.savefig(pp, format='pdf', bbox_inches='tight')
#endfor
if plot == True:
if silent == False:
log.info('## Writing : '+out_pdf_plot+' | '+systime())
pp.close()
if silent == False: log.info('### End find_stars: '+systime())
def query_mmtlog_wind(u_start, u_stop, user='******', passwd='', path0='',
silent=False, verbose=True):
'''
Query ops.mmto.arizona.edu's log for wind data.
Note: This code requires specifying the password
Parameters
----------
u_start : string
UTC start time. Formatted as 'YYYY-MM-DD HH:MM:SS'
u_stop : string
UTC stop time. Formatted as 'YYYY-MM-DD HH:MM:SS'
user : string
Username to login. Default: 'webuser'
passwd : string
Password for user. Default: ''
path0 : string
Directory path to files.
silent : boolean
Turns off stdout messages. Default: False
verbose : boolean
Turns on additional stdout messages. Default: True
Returns
-------
tab0 : astropy.table.Table
Astropy table containing young and young2 wind data
Notes
-----
Created by Chun Ly, 28 February 2017
Modified by Chun Ly, 01 March 2017
- Return tab0
'''
if passwd == '':
log.error('Must specify password!')
log.error('Exiting!!!')
return
if silent == False: log.info('### Begin query_mmtlog_wind: '+systime())
m_start = Time(u_start).to_datetime(timezone=utc_mst)
m_start = m_start.strftime('%Y-%m-%d %H:%M%:%S')
m_stop = Time(u_stop).to_datetime(timezone=utc_mst) + \
timedelta(seconds=10*60.0) # Add 10 min. to have enough buffer
m_stop = m_stop.strftime('%Y-%m-%d %H:%M%:%S')
conn = pymysql.connect(host='ops.mmto.arizona.edu', user=user,
passwd=passwd, db='mmtlogs')
cur = conn.cursor()
sql1 = "SELECT timestamp,young_wind_speed,young_wind_direction FROM "+\
"young_background_log where timestamp >= '"+m_start+"' AND "+\
"timestamp < '"+m_stop+"'"
# print sql1
n_entries = cur.execute(sql1)
results1 = cur.fetchall()
sql2 = sql1.replace('young', 'young2')
cur.execute(sql2)
results2 = cur.fetchall()
time0 = np.repeat('XXXX-XX-XX XX:XX:XX', n_entries)
speed1 = np.zeros(n_entries)
direct1 = np.zeros(n_entries)
speed2 = np.zeros(n_entries)
direct2 = np.zeros(n_entries)
for nn in xrange(n_entries):
time0[nn] = results1[nn][0].isoformat()
speed1[nn] = results1[nn][1]
direct1[nn] = results1[nn][2]
speed2[nn] = results2[nn][1]
direct2[nn] = results2[nn][2]
outfile = path0+'wind_data.tbl'
vec0 = [time0, speed1, direct1, speed2, direct2]
names0 = ('MST_time','speed1', 'direct1', 'speed2', 'direct2')
tab0 = Table(vec0, names=names0)
if silent == False: log.info('## Writing : '+outfile)
asc.write(tab0, outfile, format='fixed_width_two_line', overwrite=True)
if silent == False: log.info('### End query_mmtlog_wind: '+systime())
return tab0
