def phase_trajectory (table, sid, period='auto', outfile='', season=123,
offset=0):
""" Does just the trajectory window from earlier. """
# Loading up the relevant datapoints to plot (note I set flags to 0)
s_table = season_cut(table, sid, season, flags=0)
if len(s_table) == 0:
print "no data here"
return
date = s_table.MEANMJDOBS - 54579
jcol = s_table.JAPERMAG3
hcol = s_table.HAPERMAG3
kcol = s_table.KAPERMAG3
jmh = s_table.JMHPNT
hmk = s_table.HMKPNT
jerr = s_table.JAPERMAG3ERR
herr = s_table.HAPERMAG3ERR
kerr = s_table.KAPERMAG3ERR
jmherr=s_table.JMHPNTERR
hmkerr=s_table.HMKPNTERR
# Let's figure out the period.
if period == 'auto':
period = 1./test_analyze(date, jcol, jerr)
print period
elif period == 'lsp':
lomb = lsp(date,jcol,6.,6.)
lsp_freq = lomb[0]
lsp_power= lomb[1]
Jmax = lsp_mask( lsp_freq, lsp_power)
lsp_per = 1./ lomb[0][Jmax]
period = lsp_per
print period
if period < 1:
period_string = "%f hours" % (period*24)
print period_string
else:
period_string = "%f days" % period
phase = ((date % period) / period + offset) % 1.
fig = plt.figure(figsize = (10, 6), dpi=80,
facecolor='w', edgecolor='k')
ax_jhk = plt.subplot(1,1,1)
plot_trajectory_core( ax_jhk, hmk, jmh, phase , label='Phase')
ax_jhk.set_xlabel( "H-K" )
ax_jhk.set_ylabel( "J-H")#, {'rotation':'horizontal'})
return period
def plot_page_periods(table, sid, outfile="", name="?", season=123, png_too=False):
"""
Plot one comprehensive page of periodicity information for one source
in WFCAM time-series JHK data.
INPUTS:
table: An atpy table with WFCAM time-series photometry
sid: A 13-digit WFCAM source ID
OPTIONAL INPUTS:
outfile: an output filename, including path and filetype
extension, to save plot to (rather than plot interactively)
name: a nickname/designation for your source
season: which season to plot? 1, 2, 3, or all
OUTPUTS:
Returns nothing; optionally saves an output plot.
PROCEDURE:
This function calls the Lomb Scargle period-finding algorithm and
the Palmer fast chi-square minimization period-finding algorithm
to search for periods in the source, in each band.
Then it plots the periodogram and the lightcurve folded by the
two best periods (lomb period and palmer period).
"""
# 1. Loading up the relevant datapoints to plot (note I set flags to 0)
s_table = season_cut(table, sid, season, flags=0)
if len(s_table) < 2:
print "no data here"
return
date = s_table.MEANMJDOBS - 54579
class Band:
pass
j = Band()
h = Band()
k = Band()
jmh = Band()
hmk = Band()
kdex = Band()
bands = [j, h, k, jmh, kdex, hmk]
j.col = s_table.JAPERMAG3
h.col = s_table.HAPERMAG3
k.col = s_table.KAPERMAG3
jmh.col = s_table.JMHPNT
hmk.col = s_table.HMKPNT
j.err = s_table.JAPERMAG3ERR
h.err = s_table.HAPERMAG3ERR
k.err = s_table.KAPERMAG3ERR
jmh.err = s_table.JMHPNTERR
hmk.err = s_table.HMKPNTERR
kdex.col = 1.71 * hmk.col - jmh.col
kdex.err = np.sqrt(j.err ** 2 + h.err ** 2 + k.err ** 2)
# Done loading up data.
# 2. Compute periods and basic statistics
# a. Overall stetson variability
stet = stetson.S(j.col, j.err, h.col, h.err, k.col, k.err)
for b in bands:
# b. Lomb-scargle periodogram for each band
b.lsp = lsp(date, b.col, 6.0, 6.0)
b.lsp_freq = b.lsp[0]
b.lsp_power = b.lsp[1]
Jmax = lsp_mask(b.lsp_freq, b.lsp_power)
b.lsp_per = 1.0 / b.lsp[0][Jmax]
print "actually using timing 2"
print b.lsp_per
# deprecated:
# b.lsp_per = 1./ b.lsp[0][b.lsp[3]]
# c. Fast Chi-squared period for each band
b.fx2_per = 1.0 / test_analyze(date, b.col, b.err) # confirmed syntax
# ok, now as a test let's print these quantities that we just calculated
# print "Stetson index: " + str(stet)
# for b, n in zip(bands, ('j','h','k', 'j-h','h-k','kdex')):
# print n.upper() + " band LSP period: " + str(b.lsp_per)
# print n.upper() + " band fx2 period: " + str(b.fx2_per)
# I gotta silence the output of chi whatever. This may involve some serious popen whatever shit. (or just removing a print statement somewhere...)
# 3. Create the canvas
fig = plt.figure(num=None, figsize=(8.5, 11), dpi=80, facecolor="w", edgecolor="k")
# My first approach: using subplots rather than custom coding
qs = 3 * np.arange(6)
for b, q in zip(bands, qs): # qs: something about dimension parameters:
# b.ax1 = fig.add_axes
b.ax1 = fig.add_subplot(6, 3, q + 1)
b.ax2 = fig.add_subplot(6, 3, q + 2)
b.ax3 = fig.add_subplot(6, 3, q + 3)
b.ax1.plot(1.0 / b.lsp_freq, b.lsp_power)
b.ax1.set_xscale("log")
colors = ("b", "g", "r")
for b, c in zip((j, h, k), colors):
plot_phase_core(b.ax2, date, b.col, b.err, b.lsp_per, color=c)
plot_phase_core(b.ax3, date, b.col, b.err, b.fx2_per, color=c)
b.ax2.invert_yaxis()
b.ax3.invert_yaxis()
for b in (jmh, kdex, hmk):
plot_phase_core(b.ax2, date, b.col, b.err, b.lsp_per)
plot_phase_core(b.ax3, date, b.col, b.err, b.fx2_per)
if b is kdex:
# plot a dotted line:
xs = [-0.25, 1.25]
ys = [0.1, 0.1]
b.ax2.plot(xs, ys, "r--")
b.ax3.plot(xs, ys, "r--")
# plot red dots on disky nights:
disk = np.where(kdex.col > 0.1)
if date[disk].size > 0:
plot_phase_core(b.ax2, date[disk], b.col[disk], b.err[disk], b.lsp_per, color="r")
plot_phase_core(b.ax3, date[disk], b.col[disk], b.err[disk], b.fx2_per, color="r")
jmean = j.col.mean()
hmean = h.col.mean()
kmean = k.col.mean()
jrms, hrms, krms = j.col.std(), h.col.std(), k.col.std()
sra, sdec = s_table.RA[0], s_table.DEC[0]
sPosition = coords.Position((sra, sdec), units="rad")
sPositionString = sPosition.hmsdms()
# I'm testing an invisible big axes thing for my title
# bigAxes = plt.axes(frameon=False)
# plt.xticks([])
# plt.yticks([])
big_title = (
("Object %s.\t" % name)
+ (r"$J_{mean} =$ %.2f, $H_{mean} =$ %.2f, $K_{mean} =$ %.2f, " % (jmean, hmean, kmean))
+ "\nSeason %d \t" % season
+ r"$J_{RMS} =$ %.3f, $H_{RMS} =$ %.3f, $K_{RMS} =$ %.3f" % (jrms, hrms, krms)
)
mean_per = np.mean([j.lsp_per, h.lsp_per, k.lsp_per, j.fx2_per, h.fx2_per, k.fx2_per])
second_title = ("Stetson Index: %.1f \n" % stet) + ("Average Period: %.2f days\n" % mean_per)
# plt.title(big_title)
j.ax1.annotate(
big_title, xy=(0.025, 0.965), xycoords="figure fraction", horizontalalignment="left", verticalalignment="top"
)
j.ax3.annotate(
second_title,
xy=(0.925, 0.965),
xycoords="figure fraction",
horizontalalignment="right",
verticalalignment="top",
)
# Use text and bbox to draw the fitted periods
for b in bands:
if b.lsp_per > 0.9:
b.lsp_per_str = "period: %.2f days" % b.lsp_per
else:
b.lsp_per_str = "period: %.2f hours" % (b.lsp_per * 24)
if b.fx2_per > 0.9:
b.fx2_per_str = "period: %.2f days" % b.fx2_per
else:
b.fx2_per_str = "period: %.2f hours" % (b.fx2_per * 24)
plt.text(
0.05,
0.05,
b.lsp_per_str,
horizontalalignment="left",
verticalalignment="bottom",
bbox=dict(facecolor="white"),
transform=b.ax2.transAxes,
)
plt.text(
0.05,
0.05,
b.fx2_per_str,
horizontalalignment="left",
verticalalignment="bottom",
bbox=dict(facecolor="white", alpha=0.3),
transform=b.ax3.transAxes,
)
plt.suptitle("Position: %s, Source ID %d." % (sPositionString, sid))
j.ax1.set_title("Lomb-Scargle Periodogram", fontsize=10)
j.ax2.set_title("Best LSP period", fontsize=10)
j.ax3.set_title("Best fX2 period", fontsize=10)
hmk.ax1.set_xlabel("Period (days)")
hmk.ax2.set_xlabel("Phase")
hmk.ax3.set_xlabel("Phase")
if outfile == "":
plt.show()
else:
if png_too:
plt.savefig(outfile + ".pdf")
plt.savefig(outfile + ".png")
plt.close()
else:
plt.savefig(outfile)
plt.close()
return
def lsp_power (table, sid, outfile='', name='', season=123, png_too=False):
"""
Plots J, H, K periodograms for one star.
Inputs:
table -- atpy table with time series photometry
sid -- WFCAM source ID of star to plot
Optional inputs:
outfile -- a place to save the file
name -- a short string to display as a name atop the plot
season -- the usual
png_too -- if True, saves both a PDF and a PNG of the outfile
(note - iff True, don't give a filename extension)
"""
# Loading up the relevant datapoints to plot (note I set flags to 0)
s_table = season_cut(table, sid, season, flags=0)
if len(s_table) < 2:
print "no data here"
return
date = s_table.MEANMJDOBS - 54579
jcol = s_table.JAPERMAG3
hcol = s_table.HAPERMAG3
kcol = s_table.KAPERMAG3
# jmh = s_table.JMHPNT
# hmk = s_table.HMKPNT
# jerr = s_table.JAPERMAG3ERR
# herr = s_table.HAPERMAG3ERR
# kerr = s_table.KAPERMAG3ERR
# jmherr=s_table.JMHPNTERR
# hmkerr=s_table.HMKPNTERR
jlsp = lsp(date, jcol, 6., 6.)
hlsp = lsp(date, hcol, 6., 6.)
klsp = lsp(date, kcol, 6., 6.)
j_lsp_freq = jlsp[0]
h_lsp_freq = hlsp[0]
k_lsp_freq = klsp[0]
j_lsp_power = jlsp[1]
h_lsp_power = hlsp[1]
k_lsp_power = klsp[1]
# best periods, filtered by the lsp_mask
j_lsp_per = 1./ j_lsp_freq[ lsp_mask( j_lsp_freq, j_lsp_power) ]
h_lsp_per = 1./ h_lsp_freq[ lsp_mask( h_lsp_freq, h_lsp_power) ]
k_lsp_per = 1./ k_lsp_freq[ lsp_mask( k_lsp_freq, k_lsp_power) ]
fig = plt.figure(figsize = (10, 6), dpi=80,
facecolor='w', edgecolor='k')
ax_j = fig.add_subplot(3,1,1)
ax_h = fig.add_subplot(3,1,2, sharex=ax_j)
ax_k = fig.add_subplot(3,1,3, sharex=ax_j)
ax_j.plot(1./j_lsp_freq, j_lsp_power, 'b')
ax_h.plot(1./h_lsp_freq, h_lsp_power, 'g')
ax_k.plot(1./k_lsp_freq, k_lsp_power, 'r')
ax_j.set_xscale('log')
ax_h.set_xscale('log')
ax_k.set_xscale('log')
ax_j.set_title(name)
ax_k.set_xlabel("Period (days)")
ax_h.set_ylabel("Periodogram Power")
# bottom = 0.1
# height = .25
# left = 0.075
# width = 0.5
# ax_k = fig.add_axes( (left, bottom, width, height) )
# ax_h = fig.add_axes( (left, bottom+.3, width, height), sharex=ax_k )
# ax_j = fig.add_axes( (left, bottom+.6, width, height), sharex=ax_k )
# ax_jhk = fig.add_axes( (.65, bottom, .3, .375) )
# ax_khk = fig.add_axes( (.65, bottom+.475, .3, .375) )
# # Plot J-band:
# ax_j.errorbar( date, jcol, yerr=jerr, fmt='bo', ecolor='k')
# ax_j.invert_yaxis()
# # Plot H-band:
# ax_h.errorbar( date, hcol, yerr=herr, fmt='go', ecolor='k' )
# ax_h.invert_yaxis()
# # Plot K-band:
# ax_k.errorbar( date, kcol, yerr=kerr, fmt='ro', ecolor='k' )
# ax_k.invert_yaxis()
# # Plot J-H vs H-K
# plot_trajectory_core( ax_jhk, hmk, jmh, date )
# # Plot K vs H-K
# plot_trajectory_core( ax_khk, hmk, kcol, date , ms=False, ctts=False) # gonna update this so that it properly uses K-band main sequence line
# ax_khk.invert_yaxis()
# # Hide the bad labels...
# plt.setp(ax_j.get_xticklabels(), visible=False)
# plt.setp(ax_h.get_xticklabels(), visible=False)
# # Label stuff
# ax_k.set_xlabel( "Time (JD since 04/23/2008)" )
# ax_j.set_ylabel( "J",{'rotation':'horizontal', 'fontsize':'large'} )
# ax_h.set_ylabel( "H",{'rotation':'horizontal', 'fontsize':'large'} )
# ax_k.set_ylabel( "K",{'rotation':'horizontal', 'fontsize':'large'} )
# ax_jhk.set_xlabel( "H-K" )
# ax_jhk.set_ylabel( "J-H")#, {'rotation':'horizontal'})
# ax_khk.set_xlabel( "H-K" )
# ax_khk.set_ylabel( "K")#, {'rotation':'horizontal'})
if outfile == '':
plt.show()
else:
if png_too:
plt.savefig(outfile+".pdf")
plt.savefig(outfile+".png")
plt.close()
else:
plt.savefig(outfile)
plt.close()
def phase (table, sid, period='auto', outfile='', season=123, offset=0,
flags=0, png_too=False):
"""
Plots J, H, K lightcurves, as well as JHK color-color and color-mag
trajectories, for one star.
Inputs:
table -- atpy table with time series photometry
sid -- WFCAM source ID of star to plot
Optional inputs:
outfile -- a place to save the file
name -- a short string to display as a name atop the plot
season -- the usual
png_too -- if True, saves both a PDF and a PNG of the outfile
(note - iff True, don't give a filename extension)
flags -- whether to remove bad observations from plotting,
and where to draw the cutoff.
"""
# Loading up the relevant datapoints to plot
# (note I set 'flags' as a keyword)
s_table = season_cut(table, sid, season, flags=flags)
if len(s_table) == 0:
print "no data here"
return
date = s_table.MEANMJDOBS - 54579
jcol = s_table.JAPERMAG3
hcol = s_table.HAPERMAG3
kcol = s_table.KAPERMAG3
jmh = s_table.JMHPNT
hmk = s_table.HMKPNT
jerr = s_table.JAPERMAG3ERR
herr = s_table.HAPERMAG3ERR
kerr = s_table.KAPERMAG3ERR
jmherr=s_table.JMHPNTERR
hmkerr=s_table.HMKPNTERR
# Let's figure out the period.
if period == 'auto':
period = 1./test_analyze(date, jcol, jerr)
print period
elif period == 'lsp':
lomb = lsp(date,jcol,6.,6.)
lsp_freq = lomb[0]
lsp_power= lomb[1]
Jmax = lsp_mask( lsp_freq, lsp_power)
lsp_per = 1./ lomb[0][Jmax]
period = lsp_per
print period
if period < 1:
period_string = "%f hours" % (period*24)
print period_string
else:
period_string = "%f days" % period
phase = ((date % period) / period + offset) % 1.
fig = plt.figure(figsize = (10, 6), dpi=80,
facecolor='w', edgecolor='k')
bottom = 0.1
height = .25
left = 0.075
width = 0.5
ax_k = fig.add_axes( (left, bottom, width, height) )
ax_h = fig.add_axes( (left, bottom+.3, width, height), sharex=ax_k )
ax_j = fig.add_axes( (left, bottom+.6, width, height), sharex=ax_k )
ax_jhk = fig.add_axes( (.65, bottom, .3, .375) )
ax_khk = fig.add_axes( (.65, bottom+.475, .3, .375) )
# Plot J-band:
plot_phase_core( ax_j, date, jcol, jerr, period, offset=offset, color='b')
# ax_j.errorbar( date, jcol, yerr=jerr, fmt='bo', ecolor='k')
ax_j.invert_yaxis()
# Plot H-band:
plot_phase_core( ax_h, date, hcol, herr, period, offset=offset, color='g')
# ax_h.errorbar( date, hcol, yerr=herr, fmt='go', ecolor='k' )
ax_h.invert_yaxis()
# Plot K-band:
plot_phase_core( ax_k, date, kcol, kerr, period, offset=offset, color='r')
# ax_k.errorbar( date, kcol, yerr=kerr, fmt='ro', ecolor='k' )
ax_k.invert_yaxis()
# Plot J-H vs H-K
plot_trajectory_core( ax_jhk, hmk, jmh, phase , label='Phase')
# Plot K vs H-K
plot_trajectory_core( ax_khk, hmk, kcol, phase, label='Phase', ms=False, ctts=False) # gonna update this so that it properly uses K-band main sequence line
ax_khk.invert_yaxis()
# Hide the bad labels...
plt.setp(ax_j.get_xticklabels(), visible=False)
plt.setp(ax_h.get_xticklabels(), visible=False)
# Label stuff
ax_k.set_xlabel( "Phase (Period = %s)" % period_string )
ax_j.set_ylabel( "J",{'rotation':'horizontal', 'fontsize':'large'} )
ax_h.set_ylabel( "H",{'rotation':'horizontal', 'fontsize':'large'} )
ax_k.set_ylabel( "K",{'rotation':'horizontal', 'fontsize':'large'} )
ax_jhk.set_xlabel( "H-K" )
ax_jhk.set_ylabel( "J-H")#, {'rotation':'horizontal'})
ax_khk.set_xlabel( "H-K" )
ax_khk.set_ylabel( "K")#, {'rotation':'horizontal'})
if outfile == '':
plt.show()
else:
if png_too:
plt.savefig(outfile+".pdf")
plt.savefig(outfile+".png")
plt.savefig(outfile+".eps")
plt.close()
else:
plt.savefig(outfile)
plt.close()
return period
def arraystat_2 (table, sid, season=0, rob=True, per=True, flags=0) :
""" Calculates a complicated number of parameters for a given star.
Inputs:
table -- an ATpy table with time-series photometry
sid -- a WFCAM source ID.
Optional inputs:
season -- which season to select (1,2,3, or other=All)
rob -- also use Robust statistics? (takes longer, default True)
per -- run period-finding? (takes longer, default True)
flags -- Maximum ppErrBit quality flags to use (default 0)
Returns:
ret -- a data structure containing the computed values.
"""
s_table = data_cut( table, [sid], season=season, flags=flags )
if len(s_table) < 1:
print "no data for %d!" % sid
return None
jcol = s_table.JAPERMAG3; jerr = s_table.JAPERMAG3ERR
hcol = s_table.HAPERMAG3; herr = s_table.HAPERMAG3ERR
kcol = s_table.KAPERMAG3; kerr = s_table.KAPERMAG3ERR
jmhcol=s_table.JMHPNT ; jmherr = s_table.JMHPNTERR
hmkcol=s_table.HMKPNT ; hmkerr = s_table.HMKPNTERR
racol= s_table.RA
decol= s_table.DEC
date = s_table.MEANMJDOBS
messy_table = data_cut( table, [sid], season=-1 )
jppcol=messy_table.JPPERRBITS
hppcol=messy_table.HPPERRBITS
kppcol=messy_table.KPPERRBITS
# make an empty data structure and just assign it information, then return
# the object itself!!! then there's no more worrying about indices.
class Empty():
pass
ret = Empty()
ret.N = len(s_table)
ret.RA = racol.mean()
ret.DEC = decol.mean()
ret.chip = get_chip(date[0], np.degrees(racol[0]), np.degrees(decol[0]))
if ret.N > 4:
ret.one_chip = ( get_chip(date[0], racol[0], decol[0]) ==
get_chip(date[1], racol[1], decol[1]) ==
get_chip(date[2], racol[2], decol[2]) ==
get_chip(date[3], racol[3], decol[3]) )
else:
ret.one_chip = True
ret.Stetson = stetson.S(jcol, jerr, hcol, herr, kcol, kerr)
ret.j = Empty(); ret.j.data = jcol; ret.j.err = jerr
ret.h = Empty(); ret.h.data = hcol; ret.h.err = herr
ret.k = Empty(); ret.k.data = kcol; ret.k.err = kerr
ret.jmh = Empty(); ret.jmh.data=jmhcol; ret.jmh.err = jmherr
ret.hmk = Empty(); ret.hmk.data=hmkcol; ret.hmk.err = hmkerr
bands = [ ret.j, ret.h, ret.k, ret.jmh, ret.hmk ]
for b in bands:
# use b.data, b.err
b.rchi2 = reduced_chisq( b.data, b.err )
b.mean = b.data.mean()
b.rms = b.data.std()
b.min = b.data.min()
b.max = b.data.max()
b.peak_trough = b.max - b.min
b.mean_err = b.err.mean()
# Robust quantifiers simply have an "r" at the end of their names
if rob:
b.datar = rb.removeoutliers(b.data, 3, niter=2)
b.meanr = rb.meanr(b.data)
b.rmsr = rb.stdr(b.data)
b.minr = b.datar.min()
b.maxr = b.datar.max()
b.peak_troughr = b.maxr - b.minr
# Period finding... is a little dodgy still, and might take forever
if per:
b.lsp = lsp(date, b.data, 6., 6.) # apologies if this is cluttered
Jmax = lsp_mask(b.lsp[0], b.lsp[1])
b.lsp_per = 1./ b.lsp[0][Jmax]
b.lsp_pow = b.lsp[1][Jmax]
b.fx2_per = 1./ test_analyze( date, b.data, b.err )
# Finally we'll want to do the whole slope, distance on the JMH graph
# (until I get the fitting done, we'll have to use hmk and jmh naively)
ret.color_slope = (ret.jmh.peak_trough / ret.hmk.peak_trough)
# and the pp_max, using the messy table
ret.jpp_max = jppcol.max()
ret.hpp_max = hppcol.max()
ret.kpp_max = kppcol.max()
return ret
def statcruncher (table, sid, season=0, rob=True, per=True,
graded=False, colorslope=False, flags=0) :
"""
Calculates several statistical properties for a given star.
Will work with "lonely" datapoints (i.e. not all JHK mags are
well-defined). Optionally works with graded data, too!
Parameters
----------
table : atpy.Table
Table with time-series photometry
sid : int
13-digit WFCAM source ID of star to plot
season : int, optional
Which observing season of our dataset (1, 2, 3, or all).
Any value that is not the integers (1, 2, or 3) will be
treated as "no season", and no time-cut will be made.
Note that this is the default behavior.
rob : bool, optional
Use robust statistics, in addition to normal ones?
(takes longer, default True)
per : bool, optional
Run period-finding? Uses fast chi-squared and lomb-scargle.
(takes longer, default True)
graded : bool, optional
Also calculate Stetson indices using quality grades as weights?
Uses stetson_graded; requires that the data has been graded by
night_cleanser.null_cleanser_grader().
colorslope : bool, optional
Calculate color slopes? Runs them over (JvJ-H, KvH-K, J-HvH-K).
Make sure your data has been color-error-corrected! Default False.
flags : int, optional
Maximum ppErrBit quality flags to use (default 0)
Returns
-------
ret : data structure
Contains the computed values.
They can be accessed as attributes
(e.g., "ret.j_mean" or "ret.Stetson").
"""
s_table = data_cut ( table, sid, season=season)
if len(s_table) < 1:
print "no data for %d!" % sid
return None
# First, let's compute single-band statistics. This will require
# separate data_cuts on each band.
full_jtable = band_cut(s_table, 'j')
full_htable = band_cut(s_table, 'h')
full_ktable = band_cut(s_table, 'k')
j_table = band_cut(s_table, 'j', max_flag=flags)
h_table = band_cut(s_table, 'h', max_flag=flags)
k_table = band_cut(s_table, 'k', max_flag=flags)
jmh_table = band_cut(j_table, 'h', max_flag=flags)
hmk_table = band_cut(h_table, 'k', max_flag=flags)
# jhk_table used only for colorslope
jhk_table = band_cut( jmh_table, 'k', max_flag=flags)
# get a date (x-axis) for each
jdate = j_table.MEANMJDOBS
hdate = h_table.MEANMJDOBS
kdate = k_table.MEANMJDOBS
jmhdate = jmh_table.MEANMJDOBS
hmkdate = hmk_table.MEANMJDOBS
# date = s_table.MEANMJDOBS
# get a magnitude and magnitude error for each band
jcol = j_table.JAPERMAG3; jerr = j_table.JAPERMAG3ERR
hcol = h_table.HAPERMAG3; herr = h_table.HAPERMAG3ERR
kcol = k_table.KAPERMAG3; kerr = k_table.KAPERMAG3ERR
jmhcol= jmh_table.JMHPNT; jmherr = jmh_table.JMHPNTERR
hmkcol= hmk_table.HMKPNT; hmkerr = hmk_table.HMKPNTERR
# get the RA and DEC columns, checking for sensible values
racol= s_table.RA[(s_table.RA > 0) & (s_table.RA < 7)]
decol= s_table.DEC[(s_table.DEC > -4) & (s_table.DEC < 4)]
# Now let's get some ability to track errorful data.
# messy_table_j = band_cut( s_table, 'j')
# messy_table_h = band_cut( s_table, 'h')
# messy_table_k = band_cut( s_table, 'k')
# jppcol = messy_table_j.JPPERRBITS
# hppcol = messy_table_h.HPPERRBITS
# kppcol = messy_table_k.KPPERRBITS
# make an empty data structure and just assign it information, then return
# the object itself! then there's no more worrying about indices.
class Empty():
pass
ret = Empty()
# How many nights have observations in each band?
ret.N_j = len(j_table)
ret.N_h = len(h_table)
ret.N_k = len(k_table)
# What's the distribution of flags and nights?
js = full_jtable.JPPERRBITS
hs = full_htable.HPPERRBITS
ks = full_ktable.KPPERRBITS
ret.N_j_noflag = len(js[js == 0])
ret.N_h_noflag = len(hs[hs == 0])
ret.N_k_noflag = len(ks[ks == 0])
ret.N_j_info = len(js[(js < 256) & (js > 0)])
ret.N_h_info = len(hs[(hs < 256) & (hs > 0)])
ret.N_k_info = len(ks[(ks < 256) & (ks > 0)])
ret.N_j_warn = len(js[ js >= 256 ])
ret.N_h_warn = len(hs[ hs >= 256 ])
ret.N_k_warn = len(ks[ ks >= 256 ])
# Mean position of this source
ret.RA = racol.mean()
ret.DEC = decol.mean()
# Calculate the Stetson index...
S, choice, stetson_nights = Stetson_machine (s_table, flags)
ret.Stetson = S
ret.Stetson_choice = choice
ret.Stetson_N = stetson_nights
if graded:
# Calculate the graded Stetson index...
g_S, g_choice, g_stetson_nights = (
graded_Stetson_machine (s_table, flags) )
ret.graded_Stetson = g_S
ret.graded_Stetson_choice = g_choice
ret.graded_Stetson_N = g_stetson_nights
# Calculate PSTAR parameters
ret.pstar_mean = s_table.PSTAR.mean()
ret.pstar_median = np.median(s_table.PSTAR)
ret.pstar_rms = s_table.PSTAR.std()
# Create parallel data structures for each band, so we can iterate
ret.j = Empty(); ret.j.data = jcol; ret.j.err = jerr; ret.j.date = jdate
ret.h = Empty(); ret.h.data = hcol; ret.h.err = herr; ret.h.date = hdate
ret.k = Empty(); ret.k.data = kcol; ret.k.err = kerr; ret.k.date = kdate
ret.jmh = Empty(); ret.jmh.data=jmhcol; ret.jmh.err = jmherr
ret.hmk = Empty(); ret.hmk.data=hmkcol; ret.hmk.err = hmkerr
ret.jmh.date = jmhdate; ret.hmk.date = hmkdate
ret.j.N = ret.N_j ; ret.h.N = ret.N_h ; ret.k.N = ret.N_k
ret.jmh.N = len(jmh_table) ; ret.hmk.N = len(hmk_table)
bands = [ ret.j, ret.h, ret.k, ret.jmh, ret.hmk ]
for b in bands:
# use b.data, b.err
# if this band is empty, don't try to do the following assignments
if b.N == 0: continue
b.rchi2 = reduced_chisq( b.data, b.err )
b.mean = b.data.mean()
b.median = np.median(b.data) # dao
b.rms = b.data.std()
b.min = b.data.min()
b.max = b.data.max()
b.range = b.max - b.min
b.err_mean = b.err.mean() #dao
b.err_median = np.median(b.err) #dao
b.err_rms = b.err.std() #dao
b.err_min = b.err.min() #dao
b.err_max = b.err.max() #dao
b.err_range = b.err_max - b.err_min #dao
# Robust quantifiers simply have an "r" at the end of their names
if rob:
b.datar, b.indr = rb.removeoutliers(b.data, 3, niter=2, retind=True)
b.errr = b.err[b.indr]
b.meanr = rb.meanr(b.data)
b.medianr = rb.medianr(b.data) # dao
b.rmsr = rb.stdr(b.data)
b.minr = b.datar.min()
b.maxr = b.datar.max()
b.ranger = b.maxr - b.minr
b.err_meanr = b.errr.mean() # dao
b.err_medianr = np.median(b.errr) #dao
b.err_rmsr = b.errr.std() #dao
b.err_minr = b.errr.min() #dao
b.err_maxr = b.errr.max() #dao
b.err_ranger = b.err_maxr - b.err_minr #dao
# Period finding... is a little dodgy still, and might take forever
if per==True and b.N > 2:
hifac = lsp_tuning(b.date)
b.lsp = lsp(b.date, b.data, 6., hifac)
Jmax = lsp_mask(b.lsp[0], b.lsp[1])
b.lsp_per = 1./ b.lsp[0][Jmax]
b.lsp_pow = b.lsp[1][Jmax]
b.lsp_sig = getSignificance(b.lsp[0], b.lsp[1], b.lsp[2], 6.)[Jmax]
best_freq, chimin = test_analyze( b.date, b.data, b.err,
ret_chimin=True )
b.fx2_per, b.fx2_chimin = 1./best_freq, chimin
if colorslope:
# J vs J-H : use jmh_table exclusively
(ret.jjh_slope, a, ret.jjh_slope_err) = (
slope( jmh_table.JMHPNT, jmh_table.JAPERMAG3,
jmh_table.JMHPNTERR, jmh_table.JAPERMAG3ERR,
verbose=False) )
# K vs H-K : use hmk_table exclusively
(ret.khk_slope, a, ret.khk_slope_err) = (
slope( hmk_table.HMKPNT, hmk_table.KAPERMAG3,
hmk_table.HMKPNTERR, hmk_table.KAPERMAG3ERR,
verbose=False) )
# J-H vs H-K : use jhk_table exclusively
(ret.jhk_slope, a, ret.jhk_slope_err) = (
slope( jhk_table.HMKPNT, jhk_table.JMHPNT,
jhk_table.HMKPNTERR, jhk_table.JMHPNTERR,
verbose=False) )
# and the pp_max, using the messy table
# (slated for a re-implementation)
# ret.jpp_max = jppcol.max()
# ret.hpp_max = hppcol.max()
# ret.kpp_max = kppcol.max()
return ret