Added full processing test script and accessory files

tests/1643-1224.par

@@ -0,0 +1,20 @@
+PSRJ           	J1643-1224
+RAJ            	16:43:38.15583            4.000e-05
+DECJ           	-12:24:58.720             4.000e-03
+DM             	62.4121                   2.000e-04
+PEPOCH         	50288.0000
+F0             	216.373340849179    1      5.000e-12
+F1             	-8.657E-16                5.000e-19
+PMRA           	3                         1.000e+00
+PMDEC          	-8                        5.000e+00
+POSEPOCH       	50288.00
+BINARY         	ELL1
+PB             	147.0173943               7.000e-07
+A1             	25.072613                 1.000e-06
+OM             	321.808                   1.100e-05
+TASC           	50181.618211              1.000e-06
+EPS1           	-3.1271E-04               9.000e-08
+EPS2           	3.975E-04                 1.000e-07
+START          	49645.1250
+FINISH         	50931.5800
+CLK            	UTC(NIST)

tests/Lband.birds

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+#Freq   Width #harm  grow?  bary?
+28.760  0.1   2      0      0
+60.0    0.05  2      1      0
+

tests/dedisp.py

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+import os
+
+# To use this script to help you dedisperse a bunch of time series, first
+# run DDplan.py with appropriate values for your data to generate a
+# dedispersion plan:
+#
+# sransom@foops:~$ DDplan.py -d 200 -t 0.000072 -s 32 -n 96 -b 48.0 -f 820.0
+#
+# Minimum total smearing     : 0.102 ms
+# --------------------------------------------
+# Minimum channel smearing   : 3.76e-05 ms
+# Minimum smearing across BW : 0.00361 ms
+# Minimum sample time        : 0.072 ms
+#
+# Setting the new 'best' resolution to : 0.072 ms
+# Best guess for optimal initial dDM is 0.199
+#
+#   Low DM    High DM     dDM  DownSamp  dsubDM   #DMs  DMs/call  calls  WorkFract
+#     0.000     38.400    0.20       1    4.80     192      24       8    0.7273
+#    38.400     60.000    0.30       2    7.20      72      24       3    0.1364
+#    60.000    108.000    0.50       4   12.00      96      24       4    0.09091
+#   108.000    204.000    1.00       8   24.00      96      24       4    0.04545
+#
+#
+# Now with that plan, fill in the lists below and appropriate variables
+# for your data and you can then generate the subbands and time series
+# using "python dedisp.py"
+#
+
+
+def myexecute(cmd):
+    print("'%s'"%cmd)
+    os.system(cmd)
+
+
+# dDM steps from DDplan.py
+dDMs      = [2.0, 3.0]
+# dsubDM steps
+dsubDMs   = [48., 72.]
+# downsample factors
+downsamps = [4, 8]
+# number of calls per set of subbands
+subcalls  = [7, 3]
+# The low DM for each set of DMs 
+startDMs  = [0.0, 336.0]
+# DMs/call
+dmspercall = 24
+# Number of subbands
+nsub = 32
+# The basename of the output files you want to use
+basename = "Lband"
+# The name of the raw data file (or files if you use wildcards) to use
+rawfiles = "GBT*.fil"
+# The name of the maskfile to apply (if no mask, use None)
+maskfile = basename+"_rfifind.mask"
+
+# Loop over the DDplan plans
+for dDM, dsubDM, downsamp, subcall, startDM in \
+        zip(dDMs, dsubDMs, downsamps, subcalls, startDMs):
+    # Get our downsampling right
+    subdownsamp = downsamp/2
+    datdownsamp = 2
+    if downsamp < 2: subdownsamp = datdownsamp = 1
+    # Loop over the number of calls
+    for ii in range(subcall):
+        subDM = startDM + (ii+0.5)*dsubDM
+        # First create the subbands
+        if maskfile:
+            myexecute("prepsubband -mask %s -sub -subdm %.2f -nsub %d -downsamp %d -o %s %s" %
+                      (maskfile, subDM, nsub, subdownsamp, basename, rawfiles))
+        else:
+            myexecute("prepsubband -sub -subdm %.2f -nsub %d -downsamp %d -o %s %s" %
+                      (subDM, nsub, subdownsamp, basename, rawfiles))
+        # And now create the time series
+        loDM = startDM + ii*dsubDM
+        subnames = basename+"_DM%.2f.sub[0-9]*"%subDM
+        myexecute("prepsubband -lodm %.2f -dmstep %.2f -numdms %d -downsamp %d -o %s %s" %
+                  (loDM, dDM, dmspercall, datdownsamp, basename, subnames))

tests/process_example_data.sh

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+cd /dev/shm
+mkdir test
+cd test
+touch process.stdout
+wget http://www.cv.nrao.edu/~sransom/GBT_Lband_PSR.fil
+# cp /home/sransom/data/PRESTO_tutorial/GBT_Lband_PSR.fil .
+readfile GBT_Lband_PSR.fil 
+rfifind -time 1.0 -o Lband GBT_Lband_PSR.fil >> process.stdout
+rfifind -nocompute -time 1.0 -freqsig 6.0 -mask Lband_rfifind.mask -o Lband GBT_Lband_PSR.fil >> process.stdout
+rfifind_stats.py Lband_rfifind.mask
+weights_to_ignorechan.py Lband_rfifind.weights
+prepdata -nobary -o Lband_topo_DM0.00 -dm 0.0 -mask Lband_rfifind.mask GBT_Lband_PSR.fil
+# exploredat Lband_topo_DM0.00.dat
+realfft Lband_topo_DM0.00.dat 
+# explorefft Lband_topo_DM0.00.fft
+accelsearch -numharm 4 -zmax 0 Lband_topo_DM0.00.dat
+cat Lband_topo_DM0.00_ACCEL_0
+cp $PRESTO/tests/Lband.birds .
+prepdata -o tmp GBT_Lband_PSR.fil | grep Average
+DDplan.py -d 500.0 -n 96 -b 96 -t 0.000072 -f 1400.0 -s 32 -r 0.5 -o test_DDplan.ps
+ls -l test_DDplan.ps
+cp $PRESTO/tests/dedisp.py .
+python dedisp.py >> process.stdout 2>&1
+mkdir subbands
+mv *.sub* subbands/
+rm -f tmp.* *.tmp Lband*topo*
+ls *.dat | xargs -n 1 realfft >> process.stdout
+ls *dat | wc
+ls *fft | wc
+cp Lband_DM0.00.inf Lband.inf
+makezaplist.py Lband.birds 
+ls -l *zaplist
+ls *.fft | xargs -n 1 zapbirds -zap -zapfile Lband.zaplist -baryv -5.697334e-05 >> process.stdout
+ls *.fft | xargs -n 1 accelsearch -zmax 0 -flo 15 >> process.stdout
+cp $PRESTO/python/ACCEL_sift.py .
+python ACCEL_sift.py
+quick_prune_cands.py *DM62*0
+quickffdots.py Lband_DM62.00.fft 216.373
+gotocand.py -local Lband_DM62.00_ACCEL_0:1 -noxwin
+prepfold -noxwin -accelcand 1 -accelfile Lband_DM62.00_ACCEL_0.cand -dm 62 subbands/Lband_DM72.00.sub??
+mv subbands/*.pfd* .
+prepfold -noxwin -nosearch -n 64 -fine -nsub 96 -p 0.004621638 -dm 62.3 GBT_Lband_PSR.fil 
+prepfold -noxwin -nodmsearch -n 64 -fine -nsub 96 -p 0.004621 -o periodsearch -dm 62.3 GBT_Lband_PSR.fil 
+pfd_for_timing.py *pfd
+single_pulse_search.py *dat >> process.stdout
+ls -l Lband_singlepulse.ps
+# pygaussfit.py GBT_Lband_PSR_4.62ms_Cand.pfd
+# cat > test.gaussians
+get_TOAs.py -2 -s 2 -n 16 -d 62.3 -g 0.04 GBT_Lband_PSR_4.62ms_Cand.pfd > xxx.tim
+cp $PRESTO/tests/1643-1224.par .
+tempo -f 1643-1224.par xxx.tim 
+# pyplotres.py