Merge branch 'master' of github.com:othocaes/psdlag-agn

data/STORM_III/lightcurves/HST1367.lc

@@ -0,0 +1,171 @@
+# 0.1 1
+56691.5  3.545  0.065
+56692.4  3.771  0.067
+56693.3  3.814  0.068
+56695.3  4.094  0.071
+56696.2  4.425  0.075
+56697.3  4.53  0.075
+56698.3  4.827  0.079
+56699.2  4.58  0.076
+56700.2  4.6  0.076
+56701.4  4.746  0.078
+56702.2  4.774  0.078
+56703.2  4.756  0.078
+56705.3  4.577  0.076
+56706.2  4.47  0.075
+56707.2  4.665  0.077
+56708.3  4.324  0.074
+56709.3  4.143  0.071
+56710.3  3.769  0.068
+56711.1  3.522  0.065
+56712.2  3.476  0.064
+56713.2  3.518  0.065
+56714.2  3.445  0.064
+56715.0  3.146  0.061
+56715.9  3.058  0.06
+56716.8  2.964  0.059
+56718.8  2.675  0.056
+56720.1  2.601  0.055
+56721.0  2.376  0.053
+56722.1  2.225  0.051
+56723.1  2.187  0.051
+56726.1  2.296  0.052
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+56729.8  2.454  0.054
+56730.8  2.422  0.053
+56732.0  2.469  0.054
+56732.9  2.439  0.053
+56733.8  2.494  0.054
+56734.8  2.763  0.057
+56735.8  3.243  0.062
+56736.4  3.578  0.065
+56737.7  3.788  0.068
+56738.5  3.991  0.07
+56739.7  4.246  0.073
+56740.4  4.544  0.076
+56741.3  4.523  0.076
+56744.4  5.435  0.085
+56745.3  5.479  0.086
+56746.2  5.254  0.084
+56747.2  5.659  0.088
+56748.2  5.497  0.086
+56749.2  5.283  0.084
+56750.3  5.155  0.082
+56751.2  4.937  0.08
+56752.0  4.672  0.077
+56753.0  4.089  0.071
+56754.0  3.619  0.066
+56755.2  3.446  0.064
+56756.1  3.546  0.065
+56757.1  3.726  0.067
+56759.3  3.586  0.066
+56760.1  3.568  0.065
+56761.1  3.888  0.069
+56762.1  3.911  0.069
+56763.0  3.932  0.069
+56764.2  4.043  0.071
+56765.2  3.83  0.068
+56766.0  3.949  0.069
+56767.0  4.083  0.071
+56768.1  4.142  0.072
+56769.2  4.528  0.076
+56770.1  4.851  0.079
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+56772.0  4.965  0.08
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+56801.0  4.809  0.079
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+56803.0  4.794  0.079
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+56808.1  4.478  0.075
+56809.1  4.707  0.078
+56809.9  4.573  0.076
+56810.8  4.465  0.075
+56812.0  4.719  0.078
+56813.0  4.809  0.079
+56814.1  5.004  0.081
+56814.9  5.324  0.084
+56816.1  5.486  0.086
+56816.9  5.576  0.087
+56817.9  6.186  0.094
+56818.9  6.474  0.097
+56819.7  6.463  0.097
+56821.0  6.206  0.094
+56821.9  5.888  0.091
+56822.8  5.736  0.089
+56823.8  5.553  0.087
+56824.6  5.425  0.085
+56825.6  5.133  0.083
+56826.9  4.588  0.077
+56827.8  4.371  0.074
+56828.5  4.394  0.075
+56829.6  4.204  0.073
+56830.5  4.11  0.071
+56831.7  4.171  0.072
+56832.3  4.38  0.074
+56833.8  4.765  0.079
+56834.8  4.738  0.078
+56835.8  4.455  0.075
+56836.2  4.434  0.075
+56837.6  4.431  0.075
+56838.2  4.449  0.075
+56839.2  4.45  0.075
+56840.1  4.52  0.076
+56841.2  4.442  0.075
+56842.2  4.469  0.075
+56843.1  4.231  0.073
+56844.2  4.082  0.071
+56845.0  4.105  0.071
+56846.1  4.033  0.071
+56847.0  3.887  0.069
+56848.0  3.796  0.068
+56849.1  3.71  0.067
+56850.0  3.554  0.066
+56850.9  3.426  0.064
+56851.9  3.377  0.064
+56852.9  3.419  0.064
+56854.0  3.324  0.063
+56855.0  3.457  0.065
+56856.2  3.8  0.068
+56857.2  4.33  0.074
+56858.1  4.513  0.076
+56858.9  4.389  0.075
+56860.1  4.079  0.071
+56860.9  4.043  0.071
+56861.8  3.986  0.07
+56862.9  3.741  0.068
+56863.9  4.104  0.072
+56864.9  4.331  0.074
+56865.9  4.708  0.078

data/STORM_III/lightcurves/i_7647.lc

@@ -0,0 +1,177 @@
+# 0.1 1
+56693.8  0.99818  0.0010832
+56694.8  1.0013  0.0011449
+56695.7  1.0108  0.0010735
+56696.7  1.0136  0.0013874
+56697.0  1.0183  0.0036828
+56697.8  1.0152  0.0015205
+56698.7  1.0214  0.003556
+56699.7  1.0193  0.0039285
+56700.7  1.0248  0.00057142
+56701.6  1.0255  0.0013993
+56701.8  1.0204  0.0057308
+56702.6  1.0327  0.001377
+56703.0  1.0295  0.0058458
+56703.9  1.0341  0.0028286
+56704.8  1.0351  0.0033558
+56705.6  1.0381  0.0025162
+56706.0  1.0396  0.0033394
+56707.0  1.0394  0.0041289
+56708.0  1.0421  0.004911
+56709.8  1.0268  0.0044325
+56710.7  1.0238  0.0021402
+56711.0  1.0269  0.0057723
+56711.7  1.0219  0.0010382
+56711.9  1.0224  0.0033551
+56713.7  1.0099  0.0038844
+56713.9  1.0189  0.0036202
+56714.7  1.011  0.00047881
+56715.9  1.0075  0.0042615
+56716.7  1.0073  0.0011921
+56717.7  0.99781  0.0010252
+56718.0  1.0032  0.0090012
+56718.6  1.0009  0.0087718
+56718.7  0.98788  0.0009763
+56719.6  0.97784  0.010423
+56720.7  0.97176  0.001192
+56721.7  0.96021  0.00086336
+56722.7  0.94266  0.00073112
+56723.6  0.9498  0.0011062
+56724.5  0.92922  0.0082206
+56727.6  0.94276  0.0092891
+56728.6  0.94829  0.00078424
+56729.5  0.93688  0.00098926
+56730.5  0.94341  0.00084999
+56730.8  0.93824  0.0053844
+56731.5  0.94652  0.000662
+56732.5  0.94518  0.00059886
+56733.5  0.9465  0.00060471
+56733.8  0.94379  0.0041796
+56734.5  0.95518  0.00072721
+56735.5  0.95214  0.00063674
+56735.9  0.95989  0.0042691
+56736.5  0.96861  0.00078904
+56736.8  0.97435  0.0044905
+56737.5  0.98445  0.00084149
+56740.9  1.0188  0.0098614
+56741.6  1.0135  0.00092777
+56741.7  1.0185  0.0087678
+56743.6  1.0336  0.006135
+56744.5  1.0438  0.0011527
+56744.7  1.0422  0.007808
+56746.8  1.0507  0.0046892
+56748.0  1.0586  0.011607
+56748.8  1.0573  0.0073935
+56749.8  1.0654  0.0053101
+56752.0  1.0668  0.0065078
+56752.6  1.071  0.0013997
+56753.6  1.0614  0.0013847
+56754.6  1.0533  0.0014189
+56756.0  1.0354  0.0098934
+56756.5  1.0333  0.00084616
+56757.1  1.0437  0.011788
+56757.5  1.0391  0.00572755
+56758.7  1.0349  0.0055304
+56759.9  1.0302  0.0031799
+56760.2  1.0226  0.0077373
+56762.8  1.0162  0.0031825
+56763.8  1.0142  0.0031806
+56764.8  1.0157  0.0039904
+56765.5  1.0193  0.002708
+56765.6  1.0163  0.0010884
+56765.9  1.013  0.0037752
+56766.4  1.0072  0.0035624
+56770.5  1.0251  0.0013306
+56770.8  1.0251  0.004742
+56771.5  1.0229  0.0013331
+56772.5  1.0284  0.00074432
+56772.8  1.0347  0.0068808
+56773.4  1.0354  0.0055093
+56773.9  1.0367  0.0065486
+56774.8  1.0403  0.011588
+56775.4  1.0443  0.0052589
+56775.5  1.0462  0.0008261
+56776.1  1.0515  0.010514
+56776.5  1.0469  0.00075634
+56777.5  1.0468  0.0012233
+56778.5  1.0451  0.001329
+56779.4  1.045  0.0045924
+56779.5  1.0426  0.0010962
+56779.9  1.0364  0.0064996
+56780.5  1.0415  0.0013409
+56780.8  1.0399  0.0060786
+56781.5  1.0414  0.0013411
+56782.4  1.0339  0.0013211
+56782.7  1.0358  0.007572
+56783.5  1.0321  0.0012952
+56784.4  1.0343  0.0013026
+56785.5  1.0354  0.0011273
+56786.5  1.0373  0.0010105
+56787.4  1.0346  0.0008086
+56790.5  1.0298  0.00089144
+56792.4  1.0234  0.00064158
+56793.5  1.0263  0.0011514
+56794.5  1.0327  0.0013893
+56795.4  1.0266  0.0013657
+56796.4  1.0299  0.0016216
+56797.4  1.0342  0.0015733
+56798.4  1.0344  0.0016566
+56799.4  1.0388  0.0015688
+56800.4  1.0346  0.0012622
+56801.4  1.0319  0.00112
+56802.4  1.0336  0.00097995
+56803.4  1.0358  0.0014131
+56805.5  1.0323  0.0016691
+56806.4  1.0272  0.0010286
+56807.4  1.0338  0.0012573
+56808.4  1.0356  0.0014605
+56809.4  1.0365  0.0013149
+56810.4  1.0381  0.0014683
+56811.4  1.0372  0.001497
+56812.4  1.0398  0.001338
+56813.4  1.0392  0.0017247
+56815.4  1.0443  0.0016613
+56816.3  1.0523  0.0027328
+56816.4  1.0476  0.0014594
+56816.6  1.0492  0.0056383
+56817.4  1.0489  0.001355
+56817.8  1.0501  0.00461
+56818.4  1.0635  0.0012342
+56819.3  1.0607  0.0025741
+56819.4  1.0671  0.0013257
+56820.5  1.0676  0.0010707
+56821.2  1.073  0.0031384
+56822.4  1.0768  0.0011759
+56823.4  1.0863  0.0016316
+56824.4  1.0826  0.0017377
+56825.3  1.0887  0.0053436
+56825.4  1.0888  0.0018402
+56826.4  1.0736  0.0018112
+56827.4  1.0696  0.0016159
+56828.4  1.0676  0.0016659
+56829.4  1.0648  0.0015916
+56830.4  1.0616  0.0018272
+56831.4  1.0419  0.0016339
+56832.4  1.0473  0.0015363
+56833.4  1.0512  0.0016127
+56834.4  1.0565  0.0014259
+56835.4  1.0492  0.0015334
+56839.3  1.0496  0.0039668
+56841.4  1.0514  0.0014987
+56842.2  1.0486  0.004392
+56843.2  1.0442  0.0041289
+56843.4  1.0488  0.0015184
+56845.4  1.0415  0.0016418
+56847.4  1.0284  0.0012048
+56848.4  1.0219  0.00083962
+56848.9  1.0252  0.0065753
+56850.3  1.0311  0.0029486
+56858.4  1.0166  0.0016626
+56860.4  1.0135  0.0019027
+56861.4  1.0197  0.0013262
+56862.4  1.0128  0.0017233
+56863.4  1.0119  0.0015518
+56864.4  1.0245  0.0018702
+56864.7  1.0165  0.0086684
+56865.4  1.0165  0.0016406
+56865.6  1.0161  0.0088544

inputfiles/HST1367_i_7647

@@ -0,0 +1,10 @@
+2
+data/STORM_III/lightcurves/HST1367.lc 0
+data/STORM_III/lightcurves/i_7647.lc 0
+8 0.005 0.019 0.0425 0.07 0.11 0.17 0.24 0.4 0.603
+0
+1 1 1 0.49 0.42 0.30 0.36 1.2 -0.60 -0.89 -0.72 2.39 -0.74 -1.5 -1 -3.1 -1.3 -2.3 -2 -1.9 -1.6 -2.6 -2 -1.3 -1.8 -2.6 -1.2 0 -2 -2.7 -1.3 0.63
+0:0 0
+0
+0
+100 50 50 mcmc.dat

inputfiles/calibration

@@ -1,10 +0,0 @@
-2
-data/calibration/lc_drive.dat 0
-data/calibration/lc_1.dat 0
-1 5e-3 5e-1
-0
-1 1 1 1
-0:1 1
-0
-0
-100 50 50 mcmc.dat

inputfiles/default

@@ -1,10 +0,0 @@
-1                             
-../data/calibration/lc_1.dat 0                      
-3 1e-5 1e-4 5e-4 1e-3         
-1                             
-1 1 1 1 1 1 1 1 1 1 1 1       
-0 1                           
-0                             
-0                             
-100 50 50 mcmc.dat            
-

plots/psd_tmp.gp

@@ -4,12 +4,13 @@
 # plot 'file' using 1:2:(sqrt($1)) with xerrorbars
 # plot 'file' using 1:2:($1-$3):($1+$3):4:5 with xyerrorbars
 
-plot 'tmp.sourcePSD' using 1:($2+2):3:4 with xyerrorbars, \
-'tmp.reprocPSD' using 1:($2+2):3:4 with xyerrorbars, \
-'tmp.ccPSD' using 1:($2+2):3:4 with xyerrorbars
+plot 'tmp.sourcePSD' using 1:($2):3:4 with xyerrorbars, \
+'tmp.reprocPSD' using 1:($2):3:4 with xyerrorbars,
+#'tmp.ccPSD' using 1:($2):3:4 with xyerrorbars
 #plot 'tmp.timelag' using 1:2:3:4 with xyerrorbars
 set logscale x
 set xrange [0.005:0.603]
+set yrange [-5.5:0.5]
 # set yrange [:1]
 #    (x, y, ydelta),
 #    (x, y, ylow, yhigh),
@@ -17,4 +18,4 @@ set xrange [0.005:0.603]
 #    (x, y, xlow, xhigh),
 #    (x, y, xdelta, ydelta), or
 #    (x, y, xlow, xhigh, ylow, yhigh).
- pause -1
+ pause -1

plots/timelag_tmp.gp

@@ -8,6 +8,7 @@ plot 'tmp.timelag' using 1:2:3:4 with xyerrorbars
 #plot 'tmp.timelag' using 1:2:3:4 with xyerrorbars
 set logscale x
 set xrange [0.005:0.603]
+set arrow from 0.005,0 to 0.603,0 nohead lt 3 lc rgb 'black'
 # set yrange [:1]
 #    (x, y, ydelta),
 #    (x, y, ylow, yhigh),
@@ -15,4 +16,4 @@ set xrange [0.005:0.603]
 #    (x, y, xlow, xhigh),
 #    (x, y, xdelta, ydelta), or
 #    (x, y, xlow, xhigh, ylow, yhigh).
- pause -1
+ pause -1

pres/log

@@ -0,0 +1,10 @@
+Week 1:
+
+Given four papers to read
+Giving version 1 of the psdlag program
+spent some time exploring the program
+mostly read papers
+
+
+Week 2:
+Given calibration data in the form of light curves produced by a known transfer function

scripts/heasoft_to_psdlag.pl

@@ -6,7 +6,7 @@ use utf8;
 # outputs (stdout) a lightcurve in psdlag circa 2016 Zoghbi @ UMY input format
 
 # smallest time interval.
-my $Δt = .01;
+my $Δt = 0.1;
 # normalization factor based on inspection of data
 my $flux_norm = 1e14;
 
@@ -18,8 +18,8 @@ $throw_digits = 5 - $keep_digits;
 # Skip first line -- shouldn't need this for a single filter
 <>;
 
-#Start file with number of light curves (1) and Δt
-my $linetoprint="# 1 $Δt";
+#Start file  Δt and with number of light curves (1)
+my $linetoprint="# $Δt 1";
 
 my $num_avg = 0;
 while (<>) {
@@ -33,6 +33,7 @@ while (<>) {
         $t𝓃 += 1;
         $t𝜀 = 0;
     }
+    if ($Δt >= 1) { $t𝜀 = 0; }
 
     # Print all values for this line
     # say "$λ\t$t𝓃.$t𝜀$vals";
@@ -71,4 +72,4 @@ sub min ($$) { $_[$_[0] > $_[1]] }
 sub log10 {
   my $n = shift;
   return log($n)/log(10);
-}
+}

scripts/lc_plot.pl

@@ -6,9 +6,14 @@ use feature 'say';
 use locale;
 use Switch;
 
+# This needs to be rewritten to plot the lightcurves instead
+# of the PSD and timelags.
+
 
 # Enables debug output.
 our $debug=0;
+our #verbose=0;
+
 
 
 # This section locate the output data of interest in a

src/.smhist

@@ -1,47 +0,0 @@
-data check.dat
-read f 1
-read pow 2
-limits f pow
-box
-ptype 10 3
-points f pow
-quit
-data check.dat
-read f 1
-read pow 2
-limits f pow
-ptype 10 3
-points f pow
-box
-quit
-data check.dat
-read f 1
-read pow 2
-limits f pow
-box
-ptype 10 3
-points f pow
-set lgf = log10(f)
-set lgf = alog10(f)
-set lgf = lg(f)
-erase
-box
-erase
-limits lgf pow
-points lgf pow
-box
-erase
-limits lgf 0. 3.
-box
-points lgf pow
-quit
-data check.dat
-read 1 f
-read f 1
-read pow 2
-set lgf = lg(f)
-limits lgf pow
-box
-ptype 10 3
-points lgf pow
-quit

src/README

@@ -1,32 +0,0 @@
-
-
-
-To compile, modify the file makefile to so that libdir and incdir point to where
-alglib library and header files are installed respectively, then run: make
-
-
-FILES:
-- README: this file
-- makefile: a make file for compiling
-- main.cpp: the main file, that process the input file, print help message if
-  needed and reads the light curves files. check readLC to see the light curve
-  format.
-- mod.cpp: contains the class mod, which is a base class that uses the likelihood method. This on its own does nothing, but it is meant to be inherited by others, e.g. psd , lag , lag10
-  etc ... It is here where the likelihood is calculated, and maximized.
-
-- psd.cpp: a child class of mod to calculate psds. psd10 is similar by it
-  calculate the log10 of psd. This is better than calculating the psd directly.
-
-- lag.cpp: a child class of mod to calculate cross spectra and phase lags.
-  similar to psd. there is also lag10 that calcualte the log10 of the cross
-  spectrum plus phase lag.
-
-- psdlag.cpp: a child class of mod to calculate psd and cross spec and phase
-  lag at the same time.
-
-- inc: contains the header files.
-
-- inc/mod.hpp: the header for mod.cpp. This file has the Mod class also, which
-  is a class that holds multiple mod's used for fitting multiple light curve
-  simultaneusly, each mod fits for one light curve, and the total log-likelihood
-  is the sum of individual likelihood (i.e. product of probabilities)

src/check.dat

@@ -1,6 +0,0 @@
-2.5e-5	4.681
-5.5e-5	3.358
-8.5e-5	2.911
-1.5e-4	2.650
-2.5e-4	1.864
-3.5e-4	0.605

src/fittedlags.dat

@@ -1,6 +0,0 @@
-1.022e-01 9.694e-01
-3.260e-01 9.192e-01
-5.118e-01 9.776e-01
-3.254e-01 9.269e-01
-1.000e+00 9.659e-01
-1.000e+00 9.891e-01

src/makefile

@@ -2,10 +2,8 @@
 
 #libdir='/eos/azoghbi/soft/usr/lib'
 #incdir='/eos/azoghbi/soft/usr/include'
-libdir='/home/caes/science/psdlag-agn/src'
+libdir='/home/caes/science/psdlag-agn/src/inc'
 incdir='/home/caes/science/psdlag-agn/src/inc'
 
-
-
 psdlag:
 	g++ *cpp -o psdlag -O3 -Wall -lalglib -I${incdir} -L${libdir}

src/stdafx.h

@@ -1,2 +0,0 @@
-
-